The game leaks memory regardless of what mods you have installed. This can easily be verified by linking a debugger to the process and creating and test-launching a bunch of crafts from the VAB when you already have ships/labs in the area. Every launch, regardless of whether you end up reverting it, leaves a bunch of objects that for some reason never get cleaned up. I'm not sure if Unity's garbage collection has caveats like lost references, or what sloppiness is the reason behind this.
Eventually it uses up all the memory and begins swapping, this is immediately noticeable as recurring frame-freezing. There's literally nothing you can do about this except terminate the game process, as this causes Windows to release all the allocations, cleaning up what Squad couldn't be bothered to.