Many homes are piped for future rough-in, the vent pipe may be capped off for a future bathroom.
I would not be surprised if you had plumbing in the floor for a toilet and perhaps a tub or shower, all just waiting to be tied into that capped off vent.
Vents that go through the roof, do collect water, that normally drains all the way down.
I would repair the leak that the previous owners made, and call it good.
Mark the location, and at some point if you decide to go for another bathroom, you will know how to vent it.