I built a Squeedunk Cormrant with a big ol' "recreational" cockpit once. It was my first sea kayak, and ultimately, I sawed it out and replaced it with a tighter, recessed version. See:
http://ngc704.home.comcast.net/~ngc704/Cormorant%20Rebuild/

Having said that, there's no way it's a sin to build a boat the way you want it. In fact, I think it's a sin to build your boat the way someone else says you ought to want it for whatever reason. I mean come on, it's YOUR boat, isn't it??

One of the "daydream projects" I've been kicking around for years is to build a sea kayak as an open canoe, for a fast and fun a fishing boat. Here's a picture of a CLC Pax 20 built as such an open boat (with nylon spraydecks) for use as a solo unlimited entry in the Texas Water Safari, an annual 260+ mile river race, by my friend Doug Rhude. That's him pulling into the Victoria checkpoint, where our hero was bonking the victuals bigtime, couldn't even keep water down, but managed to pull it back together and complete his 6th finish in 67 hours. That's some serious paddling!

So yeah, build YOUR boat the way YOU want it, you have my permission. :-)