G'day Michael.   I don't know if it was or is a problem, but I solved it anyway on my recently-launched Chesapeake 17LT.   My main reason was to hide the sheer clamps inside the (enlarged) cockpit, as I'd been less than careful when epoxying them to the hull panels, and they had many unsightly clamp marks on them, which offended me.

I didn't realise so many people would bend down and stick their heads into the cockpit for a good look there, but like you I also had some early thoughts about knee contact, even though I now know that's unlikely.

I simply took a length of 'pool noodle', cut it lengthwise with a sharp razor so as to give me the appropriate cross-section (which is about 1/4 to 1/3rd of a circle) to allow it to face up squarely to both the hull side and the deck underside, and glued it with silicone along its length on both those surfaces.  

To get the right cross section, cut out a paper or card circle to the same diameter as your pool noodle (mine is 2-3/4" dia), or use a thin sliver of noodle, then cut radially across to the centre to find the best-fit cross section.   I ran the noodle from the aft bulkhead to the front cross-beam, which is in front of the cockpit.

Pool noodle is cheap (I bought mine in K Mart for under $4): ultra-light: closed-cell, therefore won't hold water (so it also gives a bit of buoyancy): and comes in many light pastel colours so I was able to select one that roughly complemented the hull colours.

You can see the effect if you look at the Archive pages here: in the pages 151 - 200 section under 'Sneak Peek' you will find some photos.  Pics 3 and 4 are fairly clear.

And finally - yes, I like the look, and plan on repeating it on my new craft (Shearwater 17S&G) now nearing completion, even though I was much more careful when handling and glueing-up the sheer clamps this time around!

More to your specific point, the small black artefact just above the blue pool noodle towards the front of the cockpit is a block of MiniCell foam, shaped and sanded to suit, which is where my own knees actually do contact the hull interior. 

Hope this helps...

Wordsmith

G'day Michael, been paddling my CH17 for a couple of years now (and boy am I tired) and have had no problem with the sheer clamps and if you have knee pads as well ,your legs should not move around that much.

Robert