You could put your .desktop files in a separate directory and just symlink them to ~/.local/share/applications. If you want to have all your aliases together, you could have a directory like Aliases or whatever and then have Aliases/desktop for .desktop launchers, Aliases/bin for scripts or binaries (and have it in PATH), Aliases/bashrc for your bash aliases (and just put source …/Aliases/bashrc in ~/.bashrc), etc.
Of course everyone has their own opinions on how to organize stuff, but this is IMHO pretty clean for what you probably want to do.
Edit: and to quickly (re)create the symlinks, you could use a bash one-liner like for f in …/Aliases/desktop/*; do ln -s “$f” “~/.local/share/applications/$(basename “$f”)”; done - put it into your bashrc as a function and remember to run it whenever you create a new .desktop launcher, and you should be golden.