Well, removing the Ship limit IS going to happen for Multiplay at some point, it will allow such things as Inferno multiplay and a lot more flexibility for Modders who want to include Multiplay missions. When that happens, it will, almost without a doubt, break compatability with older builds, at the very least to a degree where the increased traffic caused by older builds would cease to be a small issue.
Oddly enough, one of the best things that could be done at the moment, purely for optimisation and reducing server load would be to remove support for Tom's build....