Can they tell the difference between you and someone else, I believe they can. Do they miss you when you're not there, I'd have to say no.

Having said that, as was pointed out, they often respond best when things are done the same, so whilst your snake didn't miss you as such, the fact that he didn't smell you during feeding time could have come into play. My friends Boa will nip any one except him when you take it out the cage, but once he's out he's fine.

The jacobsons organ is very sensitive, so I really have no doubt they can tell by smell alone that the usual person is picking them up, and I suppose they figure that since it's always worked out before they'll be safe this time, lol.