Is your spouse’s income based on location

It's based on the value of theitems you steal.

Easy way to check this: Go to a trainer, pay them for training 1 level of a skill. Then pickpocket the money you paid them back. Then pay them for training 4 levels, and pickpocket that money back all at once. You'll see a much greater skill increase.

(Incidentally, you can use this 'exploit' to reach a fairly high level before even leaving the first village in the game.)

Ive had my items stored in my spouses house for around two weeks and they are still there, so, yes I believe containers in your spouses house are safe. EDIT: They have been there for several months now without loss. Your spouse's house is safe.