I havn't used a voodoo3 for years so my info could be wrong but I don't think it matters with the voodoo3 because it doesn't use agp texturing. I'm pretty sure I just left it as the default setting of 64mb.
I wouldnt go so far as to say it doesnt matter, but it's not nearly as influential as with other vidceo cards and it doesnt affect nealy as many spects.
As one basic example, dropping the aperture beneath 16MB on other cards will disable many of the advanced features of AGP whereas on the V3 it will have little impact as the V3 is essentially a PCI card in an AGP slot.
I'd agree though, 64MB seems pretty suitable for your system, which also happens to be the default. in general I'd suggest avoiding aperture sizes of 128MB+ on the V3 as you stand to gain no benefits with aperture sizes that large on a V3.