It's not beta related, as it's pretty much a database scaling questions, which we've gone over quite in depth (repeatedly) over in the WPMU forums.
Remember, wordpress.COM has millions of users & blogs. they're using the same software.
Is it really practical to have +90000 tables on a MySQL database, (in my case)?
Is that not a problem in itself?
You don't use one database at that size. You replicate or split them. There's three plugins that currently exist for this, including the one wp.com uses.
And the other issues is you've said you have a "good dedicated server" but you didn't give any specs at all. That big of an install, I'd probably start with two boxes, one just for mysql.
again, though, we've gone over this in the MU forums plenty of times.
maybe a forum should be created here for beta MU version 3.
there's a forum for the beta in general. MU will cease to exist, there's not a "beta MU version 3". there's just beta 3.0 with networks enabled.
Until the current MU forums roll over here, might as well go over there.