You wouldn't need to enable the snapshot daily, you just use that when you have updated the publication and need to send a new snapshot to the subscribers. You could just create the indexes on the subscriber. You will be sending the non-clustered indexes when you reinitialize with a new snapshot. If the indexes are different between the two, the indexes would be replaced on the subscriber with indexes on the publisher.
Very often, you end up with different indexes needed on a subscriber. One way to address that and keep it correct when you send a new snapshot is to not replicate the non-clustered indexes and have your won index script to run after the snapshot is run on the subscriber. If you look at the properties for the publication, then go to Snapshot, you'll see where you can include script to run before or after the snapshot. I've usually put the index script in the section to run after the snapshot.