I mean one way to get around the "missiles need logistics" problem is to go hog wild and make everything need logistics. Projectile weapons use ammo and small amounts of reactor power, energy weapons don't use ammo but loads of reactor power. Then have reactors need reactor fuel in addition to the propellant that engines use so that even energy weapons now need some sort of logistics requirement.
Or keep it simple and make MSP more of a factor, people often forget that if you don't have maintenance turned off, those weapons failures are meant to actually simulate the logistics of the beam weapons, just so happens that supplying MSP is trivial compared to missile logistics especially since you have to make MSP for ship maintenance anyways.
The advantange of the complex route is that gauss and railguns can now have an "ammo designer", which would probably be the existing missile designer but generalized. It also means that those weapons would also incur the same design costs as missiles such as magazines and whatnot (whereas the "magazine" cost of an energy weapon is the massive reactor taking all the internal space).
On a tangential note I wish weapons failures and ship maintenance were different toggles in game settings. I don't enjoy the whole overhaul aspect and micromanagement but would like my beam weapons to still have that logistics burden on them.
