Matt,
I'd prefer there not be houses in the middle of the property, but Southold was very restrictive with the site plan. KBM may have more color, but my understanding is that there was no other choice, and the developer pulled off a minor miracle getting a new golf course approved. I don't think any great hole sites were lost, and although you can see the homes from many holes, the setbacks are large enough that they really do not come into play.
I prefer to judge courses as a whole, and don't believe in trying to make individual holes perfect (or my least favorite word, fair). But since you insist, my favorite hole is 12, and my least favorite is 10.
Tim