Do they replace current recruitables, or can we have more than 9 companions to choose from? In other words, is there a way to add more rather than replacing?

No the 9 slots are hardcoded. Only replacing is possible.

I have been trying to work around this in a indirect fashion. You can refer to the alpha release of my recruit darkkender mod. There are still some kinks in the final release not affialiated with the mod itself. As tk said it is hardcoded at least with some elements. There may as of yet still be away around this but it would require alot of intricate scripting that I haven't had the time for.