Which is better for a level 6 base--obviously defence is maxed already, maxed attack or maxed shield? Which is more annoying to the top legions? It is assumed the base is being defended fully. Also tac extenders maxed out, as well as all gp extra items.

The problem with that suggestion is that for best value, your shields should be 100% upgraded which requires 10 Resitor Overcharges per module, so you need not only a good supply of credits. I would refrain from swapping out any that you can't re-upgrade. Maxed attack isn't really going to be much of a deterrent to anyone who's not bothered by max hull and max defense.

Because even a level 8 base doesn't have space for all the attack and shield modules.

Oh, heh.

Yea, really looking forward to level 9 so we can put those last 2 attack modules on the base.

There's the answer, just upgrade base to level 9 and you don't have to choose.

What about a mix of both? ie. most attack modules and a couple of shield mods. - are there any particularly negative issues with setting a base up like that?

I'd say it depends on if you have any of the holiday modules on your base.
Q-Pedd Field Generator Effect : Shield +12%
Hallows Bane Turret Effect : Attack +10%
Add modules depending on what you have, if you have both I'd probably go for shield.
At least have one shield module that isn't fully upgraded to let your members continue to upgrade with the shield drop from that one blockade.