A tricky question. It also depends on the games you want to play and which Pentium 3 you are going to use. I am by no means an Voodoo expert but I would recommend a Voodoo 3 Agp card. I am using A voodoo 3 3000 apg with my pentium 3 3 800mhz system and it works like a charm for the games I am interested in it (1997 to 1999 gaming).
Not sure if true but you can read very often that single voodoo 3 is as powerful as voodoo 2 sli set up. So if you want to have the best glide experience without having to pay a fortune for 2 voodoo 2 cards the V3 would be the better choice.
Using a single Voodoo 2 for glide and another agp card could also be a smart choice. Like you said you could play games in 32 bit with the ot her card. Having access to some other rendering features that 3dfx does not support would also be great bonus.
There is not simple right or wrong answer I'd say. it depends on your budget and the games you want to play.