I don't know enough to answer the question of whether the spoke holes are blind.
If you mean do the spoke holes thread in on one side but don't come completely through the wheel, then that appears to be the case.
If that question depends on the manufacturing process, my wheel is a dura ace wh-7850.
I don't have a caliper so I'll try that credit card trick in a few minutes.
What do you mean by "without the stress of the spokes (nipples)"?
I understand you to be saying that without spokes this kind of pressure wouldn't occur, but the spokes are on the wheel. Or do you mean that unless someone tightened the spokes when truing the wheel that kind of damage would not normally occur?
I'm sorry, I'm just not able to visualize the concept you are trying to relay to me because the terminology is new to me.
(On that note, I have no idea how to create a credit card c-clamp but I've got a bunch of old cards to ruin experimenting!)
Finally, is this something I can or should bring up with Shimano since this possible damage is occurring without any visual damage to the outside or edges?