Usually, it boils down to choice, when I work with MVC, I tend to keep separate files for all my database objects other than that I've all my database objects/model within a single file.
MVC favours the idea of separation,separate models, views and controllers from each other. Over the years i've experienced a growing pattern where individual models are kept in separate files. You can check Ext Js 4 mvc application for reference.
I've adopted this same pattern for most of my MVC based application, locating files for editing have never been easier than this and I know where exactly to find which file.
New Programmers were also able to work with the codebase, they just knew where to find what.
When not using MVC, I tend to have all my models within a single file to avoid the overhead of importing/including these files when needed.
For a bigger codebase, sticking with MVC and keeping separate files will help when it comes to maintenance and for a smaller codebase, a single file will suffice.