When modeling a member connection to the flange of wide flange columns, do people typically make a rigid link perpendicular to the column and half the column depth to impart the moment do to connection eccentricity?
No, that is a way to do it, but it's not how I do it.
There is a way to have Risa directly apply the rigid link offsets. In the member spreadsheets I believe it's called i-j offsets. You can set this to a fixed number or you can set it to a member call off for the column it is framing into, it will then automatically update the offset to half the column width. If you change the column, it will update the offset accordingly.