The ferry may be affected by weather conditions (especially during monsoon seasons).
Some reports suggest that ticketing systems or online booking may be difficult / not very user-friendly.
While you get 40 kg free, very large baggage might be problematic or more expensive.
Make sure to check what kind of visa is accepted on this ferry route — some travelers report that certain visa types (e.g., e-visas) may not be accepted "They will not accept e-visa … you should have used that same visa to enter India via any other airport"
According to some travelers, there have been cancellations or breaks for maintenance / safety