I almost always play with EXO waves( Golem and Spire Hard, and Always play Fallen Spire Campaign), and honestly if anything I find that the Botnet might be a little weak, given that if an EXO comes in, If I am not right there to make sure that it shield it is under was not the first thing that EXO hit on the way though, I often find that I am down a Botnet. I normally do play with 2-4 planets versus 9 AIs, but given you are likely to only get 1 or 2 of them at most in a whole game, it alright if they are extremely powerful. They very much are a super weapon, and balancing them for 7-7 play might make them completely worthless when you really do need them. Unless you plan on making a way for us to rebuild them, even at great cost (Buy them from the Traders? Has that been suggested before?) I don't see any real reason to make them weaker when you are talking about 1 or 2 at the most per game, and once they are gone, they are gone.
However, I might make a suggestion to help balance them out, keep them as they are, but build a fourth EXO-wave that builds based on your Golems and only charges well you have them. Make them small at first and make their only goal to remove those Golems that you control. Keep it uncapped and sooner or later you see Hunter-Killers or Motherships flying into remove your super weapons if you managed to run them that long. Maybe even make it an option like Spire/Golem-Hard(Say, call it Golems-Very Hard?) versus easy and medium? So that if people want superweapons that cost them, they basicly can get another EXO wave that wants to wipe them out when they start to use them, because they are using them. So the AI stops sending it as soon as they are gone.