Yep I'm finishing mine and even after three coats on the hull and deck a few holes were still not complete covered so filled one by one with a squeegee. Just remember to clean some eventual drips. 
 

I kinda agree with you that this is not clear on the manual.
 

Are you worried about the light or the water coming through?

Even a fully filled watertight stitch hole can allow light through. Both the glass and epoxy are transparent or translucent. If that's all the hole has in it and over it you'll see sunlight coming through. Holes under fillets are generally covered with thickened epoxy and allow less, or even no, light through. The only way to guarantee an opaque hole is to fill it with something opaque like a toothpick, leave the copper wire in or paint over it with something opaque like paint or graphite/epoxy mix.

Sunlight through stitch holes is normal and hurts nothing at all. It's nothing to worry about from a safety or structural perspective. The same pretty much goes for narrow gaps at joints, especially if they have glass over them. Gaps of less than 1/8" are structurally completely harmless as long as they're filled with epoxy (thickened or unthickened).

I've had sunlight coming through filled stitch holes and joints in all my boats. It's a normal side-effect of the method and materials. Don't worry.

Laszlo

   Laszlo right as always, the holes are almost definitely filled with translucent epoxy.  Also keep in mind that the light will disappear anywhere you paint.  I was worried about the same thing on my build, but there was no reason to fret.

I had similar concerns after coating with epoxy.  

Poking at the stich holes with a bit of left over copper wire reassured me that they had been filled up with epoxy and that they would be watertight.

Paul 

   Ran into this on my ne dory after I varnished I went around with  toothpicks and stuck them in the holes, then took painter's tape and jamed it down on the toothpick I mixed some cab o cell. And epoxy  pulled out the toothpick and squished the epoxy in the hole and 20 minutes layer pulled up the tape

   I thought it was transparent epoxy but I actually had holes. They were above the water  line but I was worried about water intrusion damaging the plywood 

   If you have actual holes you'll want to fill them, they might not have all raw wood covered by epoxy or varnish down there in the hole.  Over time with water intrusion you might get grey spots under your finish, and maybe even leading to rot.

greg27's toothpick-thru-tape method sounds intriguing.  It might save some sanding and I might try it sometime, but you have to weigh that against the time it takes to put on all the little tabs of tape and poke holes in them. 

Of course this tip doesn't help you now, post construction, but maybe next time: On all my boats I just mixed up a putty (not too thick, so it goes down into the holes easily) made out of epoxy, wood flour and cellofill that comes near to matching the color of the wood.  Then at some point soon after the stiches are all pulled walk around the boat and fill all the holes with a dab off my fingertip, then pass over with a sharp putty knife or scraper.  This last step is important to minimize sanding.  Once all the holes are filled and epoxy is cured you do want to sand just well enough to have clean wood surrounding the holes, but not so deeply as to sand the filler out of the holes - that prevents any possibilty of a "spotty" looking finish when you do the first coat of epoxy.  Anyway, the sanding you do in the normal course of getting ready for that first coat is usually more than enough to have the holes prepped. This process can be used even on holes where the surrounding wood has already been coated in epoxy.  Bottom line - doing this adds very little etra time and effort to the build, and not only don't you have open holes or translucent holes - you almost have "invisible" holes.  You'll have to look hard to find the stitch holes in the boat, and of course they are invisible when doing the "step back 10-ft" test. 

   Oh, and I strongly recommend against trying to use commercial wood filler putty.  I won't even go into all the problems I had with that.  Sure, it could/did work, but again, take my word on this and just don't do it.  The method I described above is much better.

   I filled each hole with thickened wood flour provided. I found it would sink in hole as it dried and I actually filled at least three times for a perfect fill. I don't even notice the holes now and glad I took the time to fill them. 

Bubblehead has far more building experience than I have (I'm just finishing my 1st boat), but I just wanted to register a 2nd (strong) vote *against* using off-the shelf wood filler putty.  I used (1) putty on okoume sheer panels, (2) thickened epoxy on the sapele deck and okoume hull.  The holes with thickened epoxy look nice and clean (despite no effort at color matching - the filled holes are certainly visible up close), but my putty-filled holes left blotches on the surrounding wood that were not visible until I encapsulated the wood in clear epoxy.  I'm probably going to have to paint my sheer panels (wood duckling).  That's what I get for trying to be clever, I guess.

Also...be sure to scrape the thickened epoxy-filled holes flat immediately as advised above!  I read somewhere (want to say it was R Brown's Epoxy Basics book) that it's better to leave an epoxy blob on each hole and sand it down.  I did that against my own judgment, and it turned into a real nightmare (maybe I misunderstood what I read or am exceptionally bad at sanding).  It took me many hours to sand down the countless blobs, and I ended up thinning a ring of wood around each of multiple holes, which made it harder for me to get a fair surface later without sanding into fiberglass.  I basically had to add extra epoxy to hide the lumps I left in the wood (which were far worse in sapele than okoume, now that I think about it).

   Yeah I just pulled that stunt because I'd already varnished