Each function gets its own .pyc file, but that .pyc file contains a copy of the entire controller -- the only difference between each of the .pyc files is the very last line, which has the form:
response._vars = response._caller(the_function_that_was_called)
So, even with compiled controllers, there will likely still be some benefit to keeping the controllers smaller (though less benefit than with non-compiled controllers).
Anyway, I would probably let organizational rather than efficiency considerations dictate what's in each controller. Chances are, excessively large controller files also indicate poor code/routing organization. If you keep your code well organized and your URL routes sensible, you probably won't have a lot of large controllers.
Note, you can also reduce controller line count by moving some of the logic into modules and importing (this will be even more efficient than compiling, as once a module has been imported, it doesn't need to be re-read at all).
Anthony