The reactor puts out three main forms of energy - electricity we use on-board, energy which goes through the subspace link, and heat. Additionally, most of our electrical usage also generates heat. No matter what we do, we will always emit at least a little bit of heat, since no system is 100% efficient. Additionally, as it was stated, heatsinks and thermopiles and such work by operating on a difference of heat; while we could in _theory_ use space itself as the cold end, we are still going to be radiating that heat outwards (even moreso with space)
There is no such thing, IRL, as stealth in space. Space itself is a cold emptiness, and warm objects are very easy to find if they are at all present. It might be possible that our laws of physics don't actually apply in the universe in question, but in this universe, at least, it is impossible to attain proper stealth.
Now, I mainly suggested asteroid-looking cloaking because people were insistant on an asteroid base, probably since it wouldn't look like one. Keep in mind that we would still have the heat output problem, most likely to the same degree as otherwise, so hiding ourselves in an asteroid won't mask that. However, the disadvantage to an asteroid, as stated by the GM, is that we won't be able to get it to go FTL because of how massive it is.
I then suggested the asteroid cloak idea. In space, since there is no such thing as stealth, it won't do a whole lot. It can't do anything to reduce our heat signature; in fact, it might increase it a bit more. But the main reason I suggested it was so we at least somewhat don't appear artificial. If we come across a particularily stupid enemy, our cloaking might be effective. It might also be effective if we can get near enough to a star.