i wouldn't clip them, it's torturing! also if your beekeeping methods are correct, good you really don't need to clip them, it's not that big a of a deal to lose a swarm or to now is it? it's really not fair to them. plus it might be illegal, it is around here.
about marking, there's been talking about it latelly, check the last 2 pages of treads, or do a search, one said he uses ink