Not sure what you're asking about the length. A shorter wider yak is more stable, though slower and may not track all too well. A longer thinner yak is more likely to move straighter and easier through the water, though giving up some stability and manuverablity.
If you are planning on paddling and getting out to fish often, like floating streams, a SOT is preferable. If you are going to be fishing lakes where you won't be needing to get out often, or you plan on yaking cold water, a sit in type is preferable. Although I do use my SOT on the lakes quite often and really wouldn't want a sit in type yak.