Before you start any repair, is the boat still under warranty? If it's under 2 years old, Hobie should replace the hull no questions asked. If it under 5 or 6 years, they may be willing to work with you on a prorated replaced. That should be your first course of action. If your dealer won't investigate this for you, work with Hobie directly.
You say it's a microscopic crack, but you are getting gallons of water in. It looks small when just sitting there, but it's probably flexing open when you pedal and getting bigger with every stroke. You can try Stormsure, but know that there are very very few adhesives, glues or epoxies that will stick to the polyethylene the boat is made out of and I almost 100% certain that's not one of them. If you had a hole you needed to plug in a static area, it might work fine, but for a crack, I'd say you have less then a 1% chance of a permanent or even semi-permanent fix. It won't hurt to try, but keep your expectations low.
If you want to use glue, you need to find something specifically formulated for polyethylene. Something like this
https://youtu.be/h-9yhanz5DE As far as drilling a hole, do some research on crack drill stop you can start here :
https://www.reddit.com/r/engineering/comments/6bdugb/how_does_stop_drilling_arrest_metal_crack/Certainly don't go drilling holes and try to patch with Stormsure! You'll definitely want to be in a position to fill it in with welded plastic or a specially formulated product.
Good luck.