I would have loved a mission where Shepard went to Dark Space
don't ask me how..just would have been very interesting
Personally I would have had the final encounter be out in Dark Space, Shepard leads the forces of the galaxy to retake the Citadel, activates the Dark Relay, and then travels out beyond our galaxy's horizon. At the very least it would have make the ending talk with the Catalyst have more weight about the stake of the entire galaxy what with the Milky Way literally hanging in the background.
As far as the OP's question goes I would think that the possibility does exist of Reaper stragglers being out in Dark Space when the ending(s) occurred; in fact I hope that some are still out there. I actually liked the Reapers as antagonists prior to the whole Catalyst reveal, and hopefully with it out of the way, any surviving Reapers could get back that Cuthulu-equse, puppet master vibe that the Reapers had in ME 1 & 2.
In my mind, a Reaper could have been left behind because of severe damage sustained in the previous cycle. We know that the Protheans didn't go quietly, what if a Sovereign class Reaper was decimated by one of the last surviving Prothean fleets but wasn't totally destroyed? What if other Reapers recovered their comrade's ruined hulk and towed it back Dark Space in order to effect repairs? What if the extensive damage prohibited this Reaper from participating in this cycle, but it was repaired enough to be able to fix itself while the rest of the horde descended on the Milky Way? This might sound like total plot contrivance; which in some ways it is; but it would help to fix some of the plot holes surrounding the established cannon of the Reapers, and the Catalyst's modus operandi (IMO).
The Catalyst says that it's mandate was to preserve life and maintain peace between organics and synthetics, and that the way it goes about accomplishing that task is to wipe out the advanced civilizations so that the younger races can grow while preserving the old life in Reaper form. The problem with this is that it stores this 'life' in a warship and puts said warship in the middle of open conflict thereby increasing the chances that this preserved life will be lost. That is in no way conductive to fulfilling it's mandate, why not store the harvest races out in Dark Space where no one from the galaxy can ever threaten it? This fact, coupled with the Reapers' rather poor fighting tactics (as demonstrated in ME 3) of rushing an enemy fleet head on, defecting shots with their faces, makes the whole 'preserve life at all costs' part of the Catalyst seem counter intuitive.
However, if it was shown that the Reapers actively attempted to stave off loses, and recovered their wounded then it would lend more credence to the established canon; at least in the sense that the Catalyst is not a complete moron when it comes to ensuring the survival of harvested species. If there is a massive Reaper retrofit and repair facility out in Dark Space, and that damaged Reapers are tended to, it would help bring some more credence to the Reapers' tactical aweness as villains, as opposed to just Zerg rushing everything with no concern for losses.
From what we know, the Citadel Relay was never activated, and as the OP pointed out, we never see an energy blast traveling outside of the galaxy despite its associated Relay being the point of origin for the ending explosions. With that taken into account, we can say that the Crucible detonation does not cover Dark Space, and for all intents and purposes, it looks like the wave of color acts similar to an EMP blast; traveling along the Relay network and then dissipating; there is nothing to indicate that the Destroy, Control, or Synthesis beam(s) are still present in the galaxy after the initial blast. Any surviving Reaper forces would be free to travel into the galaxy once the wave has past. As for dealing with the endings, Destroy would be the easiest to account for, Control and Synthesis could be explained that the changes affected upon the Catalyst in those two endings rendered it incompatible with unaffected Reapers; this can be seen in the game itself as the Reaper forces don't stop attacking the forces of the galaxy until after the wave hits them.
The Shepard-lsyt and the Synthesis Catalyst would essentially be running on separate operating systems from the baseline Reapers; Shepard-lyst being the personality of Shepard integrated with the Catalyst, and the Synthesis Catalyst being infused with Shepard's 'essence'. There is no reason to believe that a Reaper without a forceful software upgrade (a la ending explosions) would recognize the new intelligence, let alone take orders from it.
This leaves room for any Reaper survivors to have their own motivations and plans moving forward. What would a Reaper do now that its is no longer being directed to carry out the harvests? Would it try and work behind the scenes and use agents to try and build up a power base in the war ravaged galaxy? Would it try and undo the damage done to the Reapers in the Milky Way? There are a lot of possibilities to go, and since the Reaper stragglers in Dark Space would be severely out gunned they would have to rely on deceit and obfuscation in order to operate in the galaxy, reverting them back to their classic 'personality' while at the same time removing the plot granted 'GOD MODE' they had in ME 3.