Here's an idea. Instead of making the cpus and modules completely obsolete in the upcoming update, how about leaving the computers for Jump Drive, Scanner, Inhibitor, and Jammers(ok, maybe not jammer) in and necessary. That way if you build a ship where it's never intended to have one of those systems, it will not function directly through the core without the cpu for it. The functions could still be used through the ship core, and still make the modules unecessary, but the CPU would have to be linked to the core to "unlock" that function through the core, then have necessary chambers to upgrade/boost those functions.
The modules SHOULD be kept, maybe just renamed as decoration blocks(they're awesome). This still eliminates the need to have craptons of modules to get the function without giving every little ship, that may not need them, the functions. So you have to add a couple cpus to your bridge, no big deal, but this way you can eliminate unwanted function by simply leaving off the necessary cpu.
The modules SHOULD be kept, maybe just renamed as decoration blocks(they're awesome). This still eliminates the need to have craptons of modules to get the function without giving every little ship, that may not need them, the functions. So you have to add a couple cpus to your bridge, no big deal, but this way you can eliminate unwanted function by simply leaving off the necessary cpu.