tube, at least this is the case for my two cars. It would appear this is intended to keep water from flowing into the hole. Instead the water is able to flow a few inches to a depression or chute/channel in the plastic cover and then on into the catch basin under the front trunk lid.
The driver's side wiper shaft is like this with a drain depression at the left most end of the cover. The other wiper shaft hole is similar and there is a drain hole in the plastic through water can flow into the center catch basin. And at the far end there is a water drain chute that directs the water flow to the passenger side catch basin.
I note there is some kind of rubber seal where this plastic cover contacts the base of the windshield. It is lifted up a bit at both ends, for a few inches. I do not know if this allows water where it shouldn't be. I have never had a problem with water or even dampness in the cabin or anywhere else for that matter.
This cover is rather new on my car. The old one, the original one, cracked -- from age -- and I had it replaced.
If you have the front lid open and the covers over the battery and on either side removed and pour some water on the windshield and observe water running down on to wiring and wiper linkage, etc., this I think is wrong and suggests the cover is not installed properly or perhaps has cracked and is no longer able to keep water flowing through those chutes/channels like it should.