Nipples at the hub puts the weight closer to the center than in the rim. So there is less rotating weight in the rim. So they will feel lighter.
As far as truing, they are a pain in the ass. This year, Shimano changed their nipples at hub wheels to nipples in the rim for all the wheels they provide to the Pros. Mainly because the mechanics complained it was too hard to maintain. I expect their entire line to have nipples back at the rim next year.
If you don't true your own wheels, I guess it would be a better buy for you (but your mechanic will hate you). If you do all your own work, I'll say go with the standard nipples in the rim wheels.