A bit more info would be useful.
On what you have told us I would say no to the twin idea
- I assume it’s a small boat so should be manoeuvrable enough with a 40 or 50 anyway.
- the benefit of 1 engine failing and having a back up is some what negated if you are only operating in the harbour.
- The benefit of 2 separate fuel systems is also some what negated for the same reason
- Twin 20s are going to way more than a single 40 I suspect
- Twin 20s are going to underperforms a single 40
- Although you can service 1 at a time this means your boat will not be able to do its job properly for twice as long, it will also increase total service bill
In summary you don’t really need the benefits of twin engines but will suffer the disadvantages.
As already said Honda 4 strokes of that size are quite happy doing extensive periods of slow stuff and Yams are not generally so fond of this sort of treatment. I've got a mariner 15 on a rigiflex that does a lot of safety boat stuff in the river, its 3 months old and does seem to appreciate a few blasts every day if we do lots of slow stuff.