If you are eluding as to how unrealistic supply missions are when it comes to bases, then absolutely, I agree. If you are asking because you don't know, I guess I better explain.
There aren't fewer aliens the next time you visit a base after a smash 'n grab (assuming you kill everyone and leave one alien alive). The game is coded to repopulate the base to approximately the same levels each time you visit (there's some randomness involved to make things interesting though). You could stun and revive all the aliens in a base but there wouldn't be any more aliens the next time you visit. Say you kill all the terrorists but leave everyone else alive. Same deal, those aliens (dead, alive, stunned, whatever) will be "replaced" with a totally fresh crew (including terrorists and weapons) next time you visit whether or not a supply ship visits.
Say you decimate a base leaving a only a single soldier cowering in an upstairs room who soiled itself after you gave it a taste of it's own medicine by anal probing it relentlessly with the barrel of a Harpoon (see, there's a use for the Harpoon after all)!
Next time you visit, the base is completely fresh with a new layout, new crew, new weapons etc. You would think that a supply ship would be in charge of this, but if you visit a crashed (or landed) one there isn't extra weapons lying around, there aren't terrorists, nor are there commanders. You'll always get the same crew.
You can get creative by visiting the landed supply ship, performing the old smash 'n grab, then aborting. The ship is now magically airborne no matter if you left the place a smoldering crater or left a single soldier alive to unrealistically pilot the craft without proper training. You need to shoot the ship down, but when you visit the crash site there's a new crew of aliens, new weapons etc. How is that possible? Who resupplies the supply ship?