Im sure this has been suggested before?
It would certainly make it easier for teams with the cash, to find a NT, or U21 team player who is for sale.
The implications? - National team player value would probably go up quite a bit.
Im not really sure if it would have any implication really.
If i remember, other options were instead of having a filter on the search, just have a flag or asterix or some kind of notice on the results page stating that the player is an U21 or NT member.