Note: I wrote this thinking there was still a fan-fiction forum, so sorry I went way beyond the length of a codex entry on the explanation.
While I understand that the change to thermal clips was done for gameplay purposes, I always felt that the explanation for it was pretty lacking. Looking at the original Mass Effect's gameplay mechanics, I can safely say there would never be a net gain from trading effectively infinite ammo for effectively faster cool-down times. This is slightly addressed in ME3 by Shepard stating (during the Conrad Verner segment) that the new internal layout of the weapons allows them to hit harder (presumably longer coil chains/rails), but again, this isn't really reinforced anywhere by the mechanics. In most situations, it's a step backwards, so I feel that the justification should be a situation where it isn't. Here's my attempt at something that could be shortened down to a codex entry (assume this would have been in Mass Effect 2).
The transition to modern thermal clip heat mitigation practices arose as a matter of practicality, serving as a cautionary tale to those tempted to view weapons development as a linear process.
Following the Battle of the Citadel, Alliance forces were tasked with neutralizing remaining Geth forces in the Attican Traverse. The Geth appeared to be isolated from each other, choosing to spread their forces between what appeared to be listening posts rather than attempting the raids that had become characteristic of the earlier parts of the war. While intel gathered during the war gave the Alliance reason to believe these Geth were not truly isolated from each other, it became apparent that the disparate outposts never reinforced each other when attacked. Though the Alliance assured the public that this was evidence that the enemy was running out of resources, intelligence specialists, aware of the expendability of Geth troops, searched for a different explanation.
The first major shift in tactics began in late 2183. A previously undetected Geth outpost on Trebin deployed a weather manipulation device. This device generated a constant storms across over several kilometers of the surface, severely reducing the Alliance's ability to identify targets from orbit, while at the same time making the existence of the outpost obvious. Aware that they were likely being baited into potentially costly ground engagements, the Alliance dispatched their best operatives to neutralize the outpost.
The first team deployed to Trebin reported minor resistance under the storm, and quickly identified the device generating it. After confirming the coordinates for orbital strike, the team prepared to exfil when they discovered they'd been flanked under the cover of the storm. The team returned fire, only to discover that their weapons were already overheated. Battle telemetry of the event revealed no indication of hacking attempts, nor that any current had been forcibly induced in the firing system. The team retreated towards the center of the storm in hope that their weapons would cool down, though they never did. The Geth, seemingly immediately aware of this issue, pursued them without regard for cover, and eventually eliminated them.
Though the structure was destroyed from orbit and the remaining Geth eliminated, similar events began to be reported during engagements at all other outposts, again with no explanation for why the weapons malfunctioned. Alliance forces quickly found themselves forced to engage exclusively from orbit, which had grim implications should the Geth ever attack a colonized world again.
The breakthrough came when analysis of the first team's weapons revealed microscopic foreign matter had collected around the weapon's heat management system. Further analysis indicated this material may be of Geth origin, though how it got there remained a mystery. Using the enemy's own tactics against them, Alliance Intelligence convinced command to send a ground team with heavily monitored equipment against another outpost. The team and their weapons were recovered, and the Alliance had their answer.
The Geth had adapted nanomachines, typically used for repairing units in the field as, as an offensive weapon. These nanites were constructed using a highly advanced SiC-SiC composite, possessed precise maneuvering capabilities by using miniscule amounts of element zero, were virtually invisible, and would quickly target the heat venting sections of enemy weapons. From there, they would coat any surface used for heat transfer, effectively blocking both radiative and convective heat transfer. These nanites were coordinated by subroutines occupying nearby Geth combat units, which meant they could react extremely effectively while devoting minimal resources to processing power.
Not possessing the means to fight war at the molecular scale, and fearing the Geth were moving towards using this technology against the colonies, the Alliance began to desperately search for any means of combating this new threat. They found it in an older form of weapon construction that actually predated humanity's entrance to the galactic community. By reducing the heat mitigation systems to a single ejectible heat sink, weapons afflicted by the nanites could be restored to full operation in a matter of seconds.
This new technique proved effective, and eventually the use of the nanites became extremely rare. It's presumable that the Geth saw diminishing returns when it came to the processing power required to control the nanites versus the few seconds it would reduce a soldier's ability to fire.
Despite the disappearance of these nanites, Alliance Officials are wary to return to a weapons system with such a critical known weakness, and have instead chosen to continue use of this "new" system while other means of combating this flaw are developed. Alien governments, many of which were already shaken by the apparent vulnerability of the Citadel, were quick to adopt this change as well. Though all militaries are seeking a return to the day of internalized weapon systems, most analysts project it could be several years before research bears fruit, attributing this to the cost of repairing the damage caused by the Geth Attack on the Citadel. For areas that depend on military surplus, such as the Terminus systems, it could be even longer.
So that's that. I tried to invent as little lore about the mechanics as possible. That bit about induced current is my explanation for how "sabotage" works in ME1. The main part that's a little fuzzy to me is how the guns actually vent heat, as in ME1 they seem to be able to do it just as effectively in vacuum as they do in-atmosphere, which would seem to indicate they do it by radiative transfer. Thing is, that's characteristically pretty slow, and while I know that without any numbers that's just my gut feeling, I will point out that the ships in Mass Effect employ other methods to cool faster (something about liquid silicon droplets I think). I could try to make an argument about Mass Effect fields helping out, but then I'd have to get into the territory of how those fields affect things at the atomic/molecular level, and that's pretty much where all the space magic is in the lore.
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