Will adding more indexes speed up using RedGate SQL DATA compare?
The question suggests that the tool is being used to migrate data and not schema, which implies that you are referring to SQL Data Compare and not SQL Compare.

In which case, yes, indexes on the comparison key columns will speed on SQL Data Compare.

I've consulted the SQL Data Compare project manager, who provides the following insight: "Usually performance problems with SDC have more to do with the network connection speed to the server and/or the disk speed on the location of the temp files, neither of which are affected by having an index on the comparison key"

SQL Data Compare performance tips are part of the SQL Data Compare documentation.