We were paddlers before we were sailors. Here are some semi random thoughts you may want to consider.
Re rudders: Rudders are handy for beginners. As you gain more experience you will probably need them less and less for stearing. However, they are very nice to have when paddling in any sort of cross
wind. Some really experienced paddlers prefer a skeg, which helps with
tracking in a wind, but without the complexity of rudder and
cables.
Re length: Longer boats are faster, track better, and have more
storage for long trips. However, for casual exploration from a mothership, anything over about 15 ft should be fine.
Re type of boat: I did a bit of paddling down in
Texas, and sit atop boats were the way to go because of the hot
weather. Up here in
Alaska, no one uses sit atops (you would freeze your butt), and everyone uses a
cockpit and spray skirt. Just depends.
Re material:
Fiberglass or kevlar boats are light, but expensive and require
maintenance. Plastic boats are heavier, but cheaper, almost indestructable, and require very little
maintenance. My choice is plastic. Whatever type you choose, make sure you get inner bulkheads, or else add floatation bags.
Re
storage on a sailboat: Storage outside the lifelines sounds like trouble to me, except for short trips in fair weather. Other options depend entirely on the boat. I've seen people put them inside the lifelines, on
cabin top, on top of a
bimini etc. As you said, clearance from
sheets, etc is the issue. Our boat is really too small for any of these, so we use an inflatable on our sailboat, and use our hardshells for kayak exclusive trips. Around here there are a lot of
water taxis who transport kakakers out to prime paddling areas. Some of those guys mount car type kayak racks (for example Yakima racks) on cabin tops.
Re self
rescue: With practice it is quite possible to eskimo roll a loaded sea kayak. However, rolling is a skill that takes considerable time to learn, and must be maintained. You should learn buddy rescue methods for when paddling with someone else. Paddle float rescues are quite effective when solo, and (contrary to some reports) can be done even in choppy waves. One advantage of sit atops is that they tend to be wider and more stable, and one can re-enter from the water without too much trouble.
Other thoughts: In another thread there was a great discussion of visibility of kayakers. Get a red, orange, or yellow boat. Wear a similar
PFD. Make yourself as visible as possible. The real risk isn't so much from sailboats (they don't go so fast), as it is from powerboats. Getting run down by a big powerboat traveling at high speed would not end well!
Enjoy paddling!