The exposed screw heads are not the best look in the world but I have never had mine leak on either of my boats.  I would suggest the following:

1.  Remove the screws and clean up the old silicone.

2.  Goop up the holes and scews with new silicone and start the threads on all screws.

While everything is still loose, add another ring of silicone around the screw shanks, right under the heads.

Tighten all screws.

Wipe off excess silicone, leaving a small fillet around the heads.

Let dry and go paddling.

Hope this solves the problem.

Paul

Actually a bigger problem than slightly annoying drips is that, if you didn't do the drill-fill-drill routine, water might be soaking into unprotected plywood around those bolt holes. 

When sealing something like this, it helps if you don't squeeze ALL the silicone out from under the bolt head by tightening it completely before the silicone has cured.

Grant

You always have the option of using the foot brace mounting kit, it does not cost that much. If your hull is painted you can seal the present screw holes repaint and be done. Even if your hull is varnished it would not be too unsightly. At least this would be one sure method to stop the leak and possible future leaks. Mark

Haven't tried them myself, but aren't those no-hole mounting studs a lot more finicky to install -- especially with a deck that's making access much more difficult?  And I'd think they would also be a pain to uninstall if you later want to switch to a different set of footbraces, with a slightly different hole space pattern.

Grant

I did find it difficult to install mine on the SW 17 S&G I built. Initially my measurements were off and I have one stud still in the boat . I cut it off and sanded it down but it is unsightly . Your right in saying you have a small space to work in. As far as ever replacing them with another foot brace I have little leg room as there is so don’t see the need or advantage to ever switching them out. I used the mounting studs because I did not want to drill holes in the side of my boat. I am going to order a hybrid night heron this Fall and plan to us them again. I made a couple of errors when I put them in but learned from my mistakes and hopefully will not repeat them on my next build. Mark

On my Wood Duck I made do-it-yourself interior footbraces by epoxy-ing small blocks of Spanish cedar wood to the interior of the kayak, and then afixing the standard kit set of footbraces to the wood blocks.  Required substituting stainless steel thin machine screws for ones that come with the kit and using the screw-into-a-hole-filled-with-epoxy technique that West recommends as an alternative to screwing directly into soft wood.  But they've worked fine, and there are no through-hull holes to leak. This is not an easy fix for somebody who has already put the deck on, though.  Might just bear it in mind for the next project.  

I have built 2 with external bolts and 2 with internal.  The external are WAY more easier to locate and install.  Neither of mine have leaked yet and all I did was what the big manufactors do.  I went to my local hardware store and got a rubber washer with a 1/4" hole and an I.D. to fit the head of the screw.  Silicone is messy and is really made to use with glass