I've had a few senseis who were seriously into yoga and often did some at the start of the session. I also used to do a bit of yoga myself and found it gave me the 'relaxed energetic' feeling that is very useful for aikido. However I now do a bit of standing postures in Chi Kung to get this (as I find it easier to do on my own, whereas yoga I prefer in a group).
I don't know if you are aware, but many of the 'stretching' excercises (e.g. the wrist stretches and back stretches) are developed to establish better ki flow (the wrist exercises can be done like a chi 'pump').
If nothing else, I'm sure the yoga makes you less prone to injury (as it builds up supportive muscles and stretches your joints) and makes you more aware of when you are tense and when you are relaxed.