Depends on the configuration. Tripping a primary breaker is preferable, since that will provide protection for the secondary side breaker. If you shunt trip a main breaker on the low side, incident energy at the main breaker will still be high since it can't fully protect itself. Also, for a typical low voltage switchboard, especially group-mounted, the main breaker is generally ignored for arc flash calculations at the switchboard due to concerns regarding arc-flash propagation. No harm in tripping both high side and low side.
Also, you'll need to find room to mount the CTs. Not always as simple as it seems.
Cheers,
Dave