Given that the existing stop in Aldershot is so close, and the train only matters for cross-border travel, I struggle to dee the utility of adding a stop in Hamilton…
The stop at Aldershot is not an unchangeable law of the universe. Train 82 currently skips Aldershot, so it's not unreasonable to ask whether trains 97 and 98 could skip Aldershot as well. The question therefore becomes whether West Harbour is a more useful stop than Aldershot.
Like you said, the primary purpose of the train is to serve Niagara and cross-border travel, and for those trip purposes people from Hamilton would need to backtrack to go to Aldershot. The fact that Hamilton residents wouldn't need to take a GO shuttle bus to access the Via train is precisely the advantage of the more central station location. Aldershot is definitely better for Burlington customers, but given the relative size of the cities, there are almost certainly more customers from Hamilton who would benefit from the move than customers from Burlington who would disbenefit.
Moving the Maple Leaf away from Aldershot would separate it from the other Via services: which could have two potential downsides:
1. loss of transfers from London/Windsor Via trains
2. loss of common facilities
The Niagara-bound Maple Leaf departs Aldershot at 09:01 but the first Via train from London doesn't arrive there until 09:31, so it is already impossible to transfer to the Maple Leaf towards Niagara.
The Toronto-bound Maple Leaf arrives at Aldershot at 19:04, and the last Via train departs at 20:23 so a transfer is possible in that direction. However, given that the transfer is only possible in one direction, I doubt many people are making it.
The Maple Leaf only runs once per day, so I doubt that any dedicated Via facilities would be constructed for it at West Harbour. The stop would be an unstaffed station similar to the Grimsby and St. Catharines stops. The most I could see is Via sending one or two Aldershot-based staff members to West Harbour from 08:00 to 09:00 to assist with boarding and customer information. So there would definitely be a reduction in facilities for Via customers compared to Aldershot.
The elephant in the room for West Harbour is that it seems to be acting as an unsafe injection site, which would make it a dramatic step down in passenger comfort from Aldershot. But as Hamilton's main train station, that issue should be addressed regardless of whether the Maple Leaf stops there.
Despite those limitations, it seems like a move from Aldershot to West Harbour would be worthwhile, since it would significantly improve travel times to/from Niagara for customers to/from Hamilton.