How many people?

A self contained "mega-dungeon" ecosystem contains enough people to prevent inbreeding, I vaguely remember that the absolute minimum population for this was 2 to the tenth or eleventh power (therefore 1024 or 2048 people). This would prevent inbreeding chances from cousins, second cousins, or even third cousins interbreeding, it would even ensure multiple generations had numerous viable options for breeding without genetic complication.

But is it enough people for something to justifiably be called a "mega-dungeon", are there enough people for distinct cultures to develop? If a war broke out, how many people can we afford to lose before the population becomes unviable? I'm looking at a few interbreeding racial genotypes, and a few cultural groups that blend into one another at the edges (have a look at my Worldbuilding 101 series to get an idea of how that works).

At this stage, I'm thinking of 50,000+ citizens, divided into a couple of larger groups at about 10,000 members each, smaller groups of 2000 to 5000 members, and a few unsustainable groups (that will have to blend into a larger group, or simply die out in a few generations) of 500 to 1000 members. Maybe 10 races at most.

That's not including the hostile aliens/monsters that also inhabit the complex. 

At an average density of 10 people per square kilometre (where every square kilometre riddled with dozens of tunnels and hundreds of chambers) and with most of those people clustered into shanties where they've found fresh water sources and edible fungi patches (or farms). You could explore for days in this complex without seeing another living soul.