You can split a plugin into separate files without turning it into separate plugins.
For example in NativeVotes:
- nativevotes.sp has the core functionality of the plugin plus its natives
- nativevotes/data-keyvalues.sp has all the things for manipulating a vote handle "owned" by NativeVotes (its named data-keyvalues because the backing store may change later)
- nativevotes/game.sp has functions for individual games that NativeVotes supports as well as Game_ abstract functions that determines which function to call for which game.
That's just an example and your plugin may be done differently. basevotes is another plugin to take a look at as it consists of basevotes.sp and a separate sp file for each vote type is supports.