There's no functional reason as such that I can see why mIRC couldn't have multiple variable files, but the question becomes 'why would you need them?'. You're at 9.3k right now, has variable storage/retrieval become buggy? Which file would variables be assigned to? Even if the standard ini file storage has limitations (there used to be a 64k limit, not sure if that's still true), you don't need to store them in an ini. My variables are all stored in a separate .mrc file by themself and I'm reasonably sure mIRC wouldn't impose a limitation on that.

But do you really need 9.3k of variables? Global variables are the 'messiest' means of storage available. In another post here you mentioned your script was made of many modules, using a global variable for modules could quite easily lead to variable 'contamination' where two modules use the same variable name. You might find it more manageable if you grouped your data into hash tables - there's no meaningful performance difference for most things, it lessens the chance of name clashes between modules, and it can provide added functionality for certain types of data ($hfind()).