About the only meditation that I've done during aikido practice (on the mat, clad in dogi and hakama kind of thing) has been short meditation for, let's say, fifteen minutes; that's about it.
I do know of teachers who add a lot of meditation into their daily aikido teachings, though.
Most of the people who do aikido and meditation sort of do it "separately." One of my former teachers meditates for an hour after she gets up in the morning. One of my dojo mates has been sitting for over twenty years now. Others go on meditative retreats ranging from one weekend to one month.
If it interests you, I say pursue it. I just have never been able to sit still and meditate for very long; of course, this probably means that I need it the most, huh?