1. Which datatype should I use to represent the hash value? UUIDs are
also 16 bytes...

md5's are always 32 characters long so probably varchar(32).

2. Does it make sense to denormalize the hash set relationships?

The general rule is normalize as much as possible then only denormalize when absolutely necessary.

3. Should I index?

What sort of queries are you going to be running?

4. What other data structure options would it make sense for me to choose?

What sort of other data will you be needing to store?

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