Hi again. Ask as many questions as you like.
We've not been to HDDR, so I can't tell you anything for sure. We have had posters who have gone to HDDR, so hopefully one of them will be along with specific info.
In general, the boats on Bay Lake (the lake that MK is on) are sometimes not able to used by wheelchairs and scooters. It's not something that happens often, but it can happen. The reason for this is the water level in the lake can be either too high or low relative to the dock and the ramp will be too steep for a power wheelchair or
scooter to get on. If the water level is OK, you can just drive a wheelchair right onto the boat. The boat CMs have some little tricks they can use, like boarding the wheelchair first (when the unloaded boat floats high in the water) or boarding last (so a heavily loaded boat sits lower in the water).
When we stayed at VWL last March, there was a sign that the boats might be closed to wheelchairs and scooters because of "changing water levels". We had DD's manual wheelchair, so we just lifted her on. There are alternate ways of transportation for when that does occur. The CMs at your resort should be able to tell you how to get there if you can't use the boat.
There is a poster named Chip'N Dale Express, who is a WDW transportation CM. You should be able to find some posts from him on the Transportation Board. He is very helpful and I don't think he would mind if you send him a PM (Personal Message) asking your question.