Does NBA Live 06 have virtually all the retro uniforms?

I know that NBA Live 07 does, but I don't recall with 06.

I wouldn't say virtually all but it's got a fair few by default. Obviously with the PC version, it's possible to add new ones in via patching.

I meant for example with the Orlando Magic, do they include all the pinstriped unis from the Shaq era and then all the unis with the embroidered stars from the T-Mac era?

In Orlando's case, yes. Not every team has every single jersey they've ever worn though but every team has at least one or two home and away retros.

You can find various retro jerseys if you want to play with retros, even like 80's Lakers or 60's Celtics. Otherwise, they don't include jerseys like late 90's Blazers or neither 00's Kings.