Another way would be to generate C code from the compiled functions and find a way to join the source files into a single one, and then compile it into a single dll containing all functions, similarly to what you would get when compiling manually a LibraryLink dll in Visual C++ for example.

I will just pass the other's word, but don't ask me for details. I just hope it will give you a hint.

I don't think there is any intrinsic problem with many LibraryLink functions other than the time and resources they take to load. But once they are loaded they should not interfere or slow down due to large numbers of functions. We know cases of loading about 600 functions and this didn't stop it working, just made it slow to load. A way around that is to just load the library functions lazily. Another case has ~800 functions and loads everything lazily, which means you only pay for the functions you use.