Let him buy it! A submarine gives the party power (which they like) and helps them get in trouble (which generates more story).
The submarine is powerful.
They've invested their precious ability points into buying a submarine, so let it be worthwhile. Let them go places they couldn't go before. Tempt them with strange things underwater they wouldn't have known about otherwise. Let the purchase of the submarine feel like a success for the party. Let them have fun using it. Ask them what they've named the submarine.
The submarine has limitations.
So they buy a small submarine, then...what? Do they have to get it trucked to the lake they want to travel on? How much does it cost to move a submarine by truck? Who else is going to notice them moving it?
Once they have it in one body of water, they might have trouble getting it to a different body of water. This lake doesn't connect to that lake, but both would be a useful place for a submarine.
And how expensive is this thing to operate?
The submarine will get them in trouble.
If people can buy submarines this easily, the military will definitely be on the lookout for them. The first time they use it to get into a no-go zone, they might not get captured, but they might get noticed. The next time they try it, they'll be up against a prepared adversary.
Submarines also can fail in ways other vehicles can't. If a surface ship starts to sink, you can abandon it in rowboats. If a submarine sinks, you're likely to be trapped in a metal tube being crushed by water. Don't spring this kind of danger on them without warning, but let them make tradeoffs, deciding when it's time to invest in repairing a leak and when they have something more urgent to do.