I guess the only difference you'll find is that 5m is longer than 5yds, so if you mark your scope up in increments of 5 units you'll have a bigger gap between 45-50m than you will have between the equivalent 50-55yds.
What difference would that make?.. erm, not alot
Quite a few shooters do use metres instead of yards on their scopes.
The downside to that would be that pretty much every zero range at UK events will be set up and marked in yards, you might find that there isn't a target board set out at the range on your scope that you want to check. By that I mean, suppose you want to check your 30m zero - in all likelihood there won't be a target board set out at 30m (or 32.8 yards).
I guess the positive side to it is you won't have that problem at international events since they're mostly set up in metres.