Hi!
Personally I would lock all the users in SU10 just for safety measures.
When I implement notes, I like to have a transport order for each SAP Note, just for tracking measures. But since you have 2000 notes to implement you can allways try to aggregate some notes into a single transport order, the problem with this kind of implementation is that if you have a problem with a single transport which contains severall notes it's harder to track the issue.
Please ensure that you have a backup and someone available from functional team to provide support (Sometimes you can have some problems with SAP Objects previously modified by other Notes/Transport Orders).
Since Notes are Security Notes, I guess it will be ok.
Good luck!