You could add PSO to Steam as a non-steam game, which will give you access to Steam Input, which you could use to map practically any keys or mice controls to your controller. This would eliminate the need to use a keyboard or mouse at all. Several people have created their own configurations that you can download via Steam Input too, if you didn't want to bother coming up with your own.
Not really a direct solution to enabling the numpad keys in-game if you only use a keyboard, but if you use a controller then it's an option to completely eliminate the need for a keyboard without having to bother with other third party apps (besides typing to talk I guess).
If you only use a keyboard, then you might be able to use something like Auto Hot Key to essentially remap the numpad keys to the regular number keys on the keyboard, but you'll need to write a script for that. Should be relatively easy though.