Hopefully, you are just doing day trips. Those familiar with the Assateague back country camp sites usually only went there once in the summer bug season. Subsequently, they wait for the notoriously viscous bugs to die off.
Chincoteague Bay and Sinepuxent Bay lay west of Assateague Island. The boat launch at Assateague National Seashore is called Ferry Landing and it is roughly on the edge of both bays. Sinepuxent lies to the north, starting at Ferry Landing and running about 8 miles north to Ocean City. Chincoteague Bay extends south from Ferry Landing down to Chincoteague Island, about 26 miles.
I've paddled Chincoteague Bay a few times a year for the last ten years. It is frequently windy. The northern half of Chincoteague Bay is mostly waist deep or shallower. Depending on the tide and more importantly the direction and force of the wind, it can get boat-dragging shallow. Because it is shallow, there is a theoretical limit to how big a wave you can get. Wind waves tend to be no more than 1 - 2 feet, but steep and high frequency. On the Chincoteague Island end, you find deeper water and bigger waves, but less steep and lower frequency. There really isn't much current to deal with until you get into the passages at Chincoteague Island.
I've not paddled Sinepuxent Bay. It is much narrower than C. Bay: 0.5 to 2 miles for S. Bay whereas C. Bay is 5 or more miles wide. The northern part of S. Bay is the narrowist, and it is close to the Ocean City inlet, so my guess is there is more water moving through it on tidal exchanges, and that might keep the water a little deeper, giving potential for bigger waves. But it is narrow enough that you should be able to work a lee shore.
Hope that helps.
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