My shoulders and arms fall asleep at night while I sleep. Will this have any long term effects? I am worried about it causing blood clots.

Sleeping habits. It may be that you are falling asleep on top of your arms, or with your neck in a crooked position, causing compression of a nerve. If a nerve is compressed for long enough, you will develop paresthesias, the medical term for "pins and needles." this improves with changing position or shaking the affected arm. Changing your pillow or sleeping surface may reduce falling asleep on your arms.