Personally I would go for two files - then you can add a third when you support Mac, and a forth when you support Symbian, and so on. It is just easier to maintain. I don't know of another module on CPAN that does things like that, I use a condition use. Here are some examples:

use if ($^O eq "MSWin32"), 'Win32::Process';
use if ($^O eq "MSWin32"), 'Win32::SearchPath';

use if ($^O ne "MSWin32"), 'POSIX';
use if ($^O ne "MSWin32"), 'POSIX' => ':sys_wait_h';

# Hack to allow compilation under Unix 
# (NORMAL_PRIORITY_CLASS and INFINITE are Win32 only)
use if ($^O ne "MSWin32"), 'constant' => 'NORMAL_PRIORITY_CLASS';
use if ($^O ne "MSWin32"), 'constant' => 'INFINITE';
[download]

Your idea of sub-modules under a "master" namespace seems reasonable to me.