Merits do make a difference, I have +6 katana skill and I notice each upgrade as I get it, so unless you're a little slow, you'll notice it. The difference when you get 6 merits in a weapon is significant. Just think of it this way, it's +12 skill, which is give or take 2-3 levels for a lot of weapons. This means you're hitting at level 77/78 when you're 75. And thus, there is a difference.
As Nny was saying, a WAR75 in my LS meritied 6 H2H upgrades for when he was leveling MNK...he was a beast. So if you want to do something like that it's an awesome idea...but expect to die a lot if you're doing it on MNK