I've had no issues. Honestly, I rarely use it. They say it can come out of the water if there are large bow/stern waves. I haven't used it in waves large enough for that. Most of the time I use it for low wind situations, and sometimes to get in and out of a difficult docking situation. I've heard long has more drag, but I doubt it's much, and you're not excactly speeding along anyway. I think I may have benifited from a short in having to get off a lee shore--basically push off and try to motor away before being blown back into shore. Shorter shaft less likely to hit bottom. Other factors--I'm heavy and generally sit neer the motor when using it, probably pushing it down further into the water. Also, it will drag a bit in the water when heeled, with the shaft pointed down a bit when it is in the up position. Longer shaft may drag a bit more.
I'm not sure if I'll sail this weekend--it's looking like wind may be exessive. I have the boat in a storage yard, but if I take it out I'll take a picture of it (if I remember) and it may help you determine what is best for you. Hope that helps!
Tim