As for nukes, I have my doubts that Reapers (or any modern starship)
would lack full hardening against EMP. If they did lack for such, they
could never operate in space outside the safety of a planetary magnetic
field. There is tons of natural EMP in space, for example from stars.
Nuclear weapons do not produce an EMP unless they are bursted in high altitude, where they interact strongly with the magnetosphere. Low altitude bursts and nukes detonating in space do not produce any emp at all.
Thermal
damage from nukes might be less effective they we would hope because
ships are designed to survive engagement with high-energy laser
batteries. Ablative armor is mentioned in the lore, and the lore, in my
opinion, seems to suggest that lasers are generally ineffective as
primary weapons because ships are sturdy enough against thermal attack
that they just don't inflict enough damage. To support this I point out
again that Nothing Dodges a Laser and that the best mass effect cannons
fire at sub-2% of c AND lasers ignore barriers... so if lasers could
actually deal meaningful damage in this universe they would immediately
replace mass effect cannons. All this leads me to believe that nukes
will probably be RDM Galactica-strength in ME - they'll knock you around
but are not really that much more devastating ship to ship than your
main gun batteries.
Actually, lasers weapons are not used as main guns because they have extremely inferior effective range. They are only good for a few tens of kilometers according to the codex (that means they must be pretty weak, based on laser intensity calculations) or 80+ KM in the case of Salarian UV lasers.
We have no instances of a weaponized laser, so we can't comment on how effective they are against armor. Regardless of that though, surface detonations of atomic weapons will dump orders of magnitude more energy than a laser strike would, all over their hull. Even if they somehow survived that, it would fry all external optics on the ship and give any crew a pretty lethal dose of radiation.
But like I posted above you, conventional nukes aren't what we should use anyway. Casba Howitzer style weapons are
nuclear shaped charges. As in, they don't explode spherically, they pump >85% of their energy into a small cone, which superheats tungsten, turning it into plasma and firing it forward at a significant speed! It's a massively powerful one-shot particle beam!
The Thanix gun shoots molten metal at a high speed. This shoots superheated metal at an extreme speed, and since the nuclear device is providing the energy, you can literally dump
megatonnes of energy into each shot!The thanix gun reportedly has "cruiser level firepower", and a Dreadnought is only 38KT! That's an improvement of multiple orders of magnitude in firepower!
Also keep in mind that while there is
a nigh unlimited amount of iron, aluminum, tungsten whatever for mass
accelerator slugs they is indeed a finite quantity of fissile material.
Mass nuclear cruise missiles may not be logistically feasible, either
for lack/expense of plutonium or of anti-matter or eezo to propel them.
It was possible for the United States and Russia to mass produce nuclear weapons at an impressive rate. The peak US stockpile was 31,000 devices in 1967, implying a production rate of nearly 4 warheads per day assuming the first device was built on January 1, 1945. Actually the rate of production through the 1940's was far lower than that of later, so the actual effective rate of production is more like 6-7 per day.
Now consider that the Systems Alliance, the smallest council race (assuming the council was saved), has more than a dozen developed colonies, numerous mining outposts and the combined wealth of the entire Earth.
I'm pretty sure they can handle mass production of nuclear bombs!