you can also use a combination of both methods, just use staples in the really tough spots and hide the tiny holes with putty and stain etc.. with putty, stain, and artist brush, you can hide those holes so that know one would ever see them, I know, I have been woodworking for 20+ years, but it would take for ever to hide a zillion holes, probably about the same time it would take you not to have them in the first place.

I was going to use staples at first, although I wanted a great looking woodstrip kayak, my primary reason for building one was to get in the water as fast as possible and paddle it. I decided to go staple-less because this might be the only kayak I will ever build, I made up my mind to take the extra time, thought it would be harder than it really is and its moving along at a good pace.
One thing I'm doing that's helping me a great deal is, I cut up a rubber tire tube, drilled holes in various places along the outer rim of each form and anywhere I need a strap to hold the strips, I insert a #16 nail in the hole and tie a rubber strap to it and loop it over the row of strips...dont know if I explained that well enough but it works great, if you need a little more holding power you can insert a wedge at various spots..I also used screws with washers on them to hold the first strip on the shear line, I put screws with washers on them just off the shear/l on all the forms and put the first strip on the line and cinched it down with the screws and washers, that held it very well.(screws in a small block of wood would work as well)..I'm well into the stripping of the hull and so far, I dont see anything that's hard about going staple-less, just takes a little more time. (if I could find my staple gun) I wouldnt hesitate to staple a really tough strip.
If I was planning on using staples on all the strips and then puttying all the holes and staining them ..I just wouldn't use staples, it would take about the same amount of time.
On the other hand, the only way anyone would ever point the staple holes out is if you had a staple-less kayak right beside a stapled one. I dont see anything wrong with either method, just a matter of personal choice and esthetics.

"--es·thet·ics 1. The branch of philosophy that deals with the nature and expression of beauty, as in the fine arts. 2. The study of the psychological responses to beauty and artistic experiences. 3. A conception of what is artistically valid or beautiful 4. An artistically beautiful or pleasing appearance."

As far as the glue gun, I cant see how that would hold anything but I never owned one so hard for me to say.