Is there a way to figure out what percentage of entries in PDB have SS bonds? In addition, what other types of bonds in PDB may be worth looking into (not H bonds)?
The easiest way is to check annotations in mmCIF or PDB files.
Looking at my page with statistics of mmCIF tags, last updated in March:
_struct_conn_type.id 59137×metalc 42706×covale 36195×disulf 10725×hydrog _struct_conn.conn_type_id 5350402×hydrog 1733277×metalc 559092×covale 226472×disulf
Which means 226472 disulfide bonds in 36195 PDB entries at the time when the PDB had 161470 entries.