server 1: 1 domain with 1000 email boxes.
server 2: 1000 domains each with 1 email box.

Will there be any different in performance?

Thanks

Your server 1 will have more load and hence the performance will be low.

It depends on which resources gets used the most. A good box should be able to handle all those email accounts, but make sure the server software can handle them.

If the domains rarely get hit that there is no overhead on the server,

my experience is an average of 10-15 emails per mailbox per day

so 1000 domains (non-corporate) is no load, either way, on the server

I would guess that option 1 would be better, because there would be less overhead in dealing with which domain the account goes with.

I would suggest for server 1 only. :)