Your first sentence seems the more colloquial and natural, regardless of whether you're talking about one pair of shoes or several. "These shoes are in size ten" would sound unnatural to me, a native U.S. English speaker, in any context. So would "these shoes are a size ten." It may be a matter of generational or regional speech, but you'll be safe anywhere using your first example ("these shoes are size 10").

1. These shoes are size ten - if you are referring to many pairs of shoes. 1. These shoes are a size ten - if you are referring to one pair of shoes. 2. I'm looking for a pair of shoes in a size ten.

"These shoes are a size 10" is how I would say it :)