He'll be fine
i've done a hamster on a train before, no problem at all, I think they just get on with it once they've worked out nothing is going to hurt them.
The idea of covering the carrier is a good one, just so he can get some kip. That said, he would in theory be asleep during the day anyway.
I've also done long distance travel on a train with 3 guinea pigs in a travel carrier, including across London on the tube. All I will say is keep your wits about you (obviously) and just remember to keep him level. Escalators (I hate them!) are a bit fun with a full size guinea pig 3 box, but with your little hammy carrier you'll be fine. I found the train ticket was a bit of a pain, on the tubes it pays to have it handy. Typically I had no pockets, so I popped it in my bra!