Thank you very much guys, I made as you said, and I was finally able to edit an already existing vessel. The modifications took longer than I would have expected for the simple addition of a couple of mystery goo containers, but lesser than it would have taken if I had to build everything from scratch, and since I had already built it, I was given back the money of the base-module (pod plus parachute and engine).
Summing up, it seems that the quickest option is still to assemble our vessels all at once, especially at the beginning of the career when we only build basic designs and even the addition/ removal of a tiny single part can make a big difference but, then again, I suppose that this can vary greatly, depending on the settings an formulas that we can customize to our liking in mod difficulty settings.
Are my conclusions correct?
Probably due to my light mod load out, I didn't experience any stutter in the VAB but I am glad that you are supporting your mods so actively!