If this boat is a typical, skin on frame style canvas covered kayak (as opposed to something with a fully planked hull) it's not a matter of what is desired, it's a matter of what will or won't work. Fiberglass is not a good material for spanning large unsupported spaces unless you make it thick enough that it would stand alone with no frame (essentially like a typical fiberglass kayak). Canvas and similar, fabric covering materials (aircraft Dacron, nylon, rubber raft fabric, etc.) will bridge spaces between frames because they flex and give as needed to survive the forces that push and pull on the skin.Trying to mix the two types - the rather rigid nature of fiberglass and flexible canvas, would be a formula for disaster. It would be heavy, weak and most likely delaminate and crack.
Smoothing fiberglass is just a matter of burying the cloth weave with extra coats of resin until you can sand it smooth without cutting the fibers. It's not particularly difficult to achieve a perfectly smooth outer surface, but it would be far too brittle to survive the type of flexing that a suspended skin gets. It needs something solid behind it (either something like wooden planking or enough extra material to make a rigid hull).
The skin smoothness of skin-on-frame kayak hulls is a matter of two things - (1) how smoothly or coarsely the cloth skin is woven, and (2) What you paint on it to seal it and how well it covers or fills the weave. Best bets for something like canvas are flexible coatings like brush-on Hypalon rubber (great stuff, but pricey) or flexible paints. The most affordable flexible paint is probably acrylic latex house paint. With every coat, the surface will get a little smoother, though the amount of flex that the surface can take without problems will likely diminish a bit. There is bound to be some sort of ideal point, where the paint has filled and smoothed the weave somewhat, yet still maintains reasonable flex and durability. Exactly where that point is, I can't tell you. Latex is not a perfect solution, but it's not awful and it's cheap and easy to find. People have been using house paint on home-made canvas kayaks for 50 years or better. Airplane dope will also work, but is pretty nasty stuff to work with. Gaco-Flex and some of the paints made for rubber rafts would also probably work but are expensive. Most standard canoe fillers don't flex enough for the job and would crack in use.
If you really can't stand the canvas texture and have to have a smoother skin, you might think about covering it with heat-shrink Dacron. It's finely woven and quite smooth, but you would lose a rather large amount of tear strength and puncture resistance, especially with a suspended skin.