You have to remove the stock aircraft names from the mdlname.txt file before you remove the stock models from the AIRCRAFT folder. If you only remove the stock models, CFS2 won't start because the mdlnames.txt file is telling CFS2 to look for them. Be aware though, many add on aircraft use the sound files from the stock aircraft as a proxy. If the addon aircraft doesn't find the stock aircraft sound file, it won't start.
Personally, I remove everything from the stock aircraft folders EXCEPT for the sound folder. Then I do not need to be concerned about a missing sound folder, I don't need to remove the names from the mdlnames.txt file, and the stock aircraft folder does not count in the total aircraft limits.