Should work fine.

Make 'em so they can be removed easily for cleaning, make sure the 'floors' they're attached to bear snugly against the panels so whatever weight's on 'em's spread well.

I'd avoid plywood for floorboards. For the same weight of solid wood, ply's less stiff owing to its cross-grain, laminated structure. Ply, thick enough for the floors you'll mount your floorboards onto, ought to accept fasteners OK if it's 1/2" / 12mm yet I'd still opt for solid wood for such light work as what you may want to achieve for this.

You'll raise your loaded CG a bit; for the convenience for stowage and keeping things dry that ought to be tolerable. Good luck with your inspiration!

   I certainly agree with spclark that if you put in some wooden floorboards, go for solid wood.  You can decide whther to make them permanently installed, easily removable, or simply unsecured/drop in place.  Any nice, light straight grained wood should work - pine, spruce, cedar, etc..  You shouldn't really have problems with rot in this application (especially if whatever wood you use is varnished or epoxy coated/varnished), but very long term durability might be enhanced by using mohagany or teak or cyprus - you pay some weight penalty but gain rot resistance.

With all that said, if you haven't already noticed, take a look a pictures 23 and 26 of the Sasafrass 16 photo gallery here on the CLC website for some additional ideas.  One shows a wooden box loaded into a fully packed canoe, the other a strap (instead of floorboard) "false bottom" solution.

Myself, I might just opt for what most canoe voyagers opt for: If portaging, an external frame backpack or old-fashioned pack-board placed frame down ususall suffices to keep a lot of things out of the water.  Wether portaging of not, mid-grade coolers (without ice! - and high end coolers just weigh more for this application, if you're not interested in dual use as a cooler) make good travel-boxes and have decent handles.  And you can spend very little on rubbermade tubs - wrap a strap around to ensure you can't lose the lid - or you can spend more if you upgrade to fancier storage boxes.  You can always buy the cooler or tub or box in dimensions that fit right where you intend to place it in the canoe.  Or consider making a custom box for the boat.  All of these solutions make loading and unloading very quick - the more gear that is "pre-packaged" as opposed to loosely stowed will save time whether simply out for a quick paddle or day picnic or on a overnight trip, and helps things stay dry.  Of course some items that don't mind getting wet can be individually stowed to help fill in the voids and make good use of space.

As always, report back on how things go for you!