By rules modifications as of 6/24/2014, there is no maximum limit of shelved navis allowed for a player. While the number of possible shelved characters is infinite, the number of teams in play remains limited by the total level milestones. You must wait a week following a shelving before you can swap a pair between the shelf and active slots again. Additionally, the staff reserves the right to decline registrations we deem unreasonable in number or frequency of registration.
Replacing the old text:
There is a maximum of 4 shelves allowed, or a total of 5 character pairs. You must wait a week before you can switch an active and shelved pair.
Between shelving and simultaneous RP, you may never have more than 5 Navis. That is, even once you can simultaneously RP 2 Navis, and you had four on the shelf, that does not mean you can make a new one to fill your new active slot while keeping those four shelves. In effect, each new pair replaces one of your shelves.
Please note: this does not mean you will be able to RP more teams of characters simultaneously. Those rules remain the same: reach the total level milestones to gain the ability to RP more teams simultaneously, up to five. This simply expands the shelf space you have for navi teams.