These two sentences don’t have the same meaning.

In Le bon bateau, “le bon” means “the right/correct one”. It better be the right boat, this time. Like they’ve been looking for a boat, and have been stumbling across a few, always the wrong one.

“Un bon bateau” on the other hand means just that, a good boat. It better be a good boat, this time. (ie not a crappy boat like last time).

Both

C’est dommage que bon nombre de photos …

and

C’est dommage qu’un bon nombre de photos …

are equivalent and idiomatic, the first one is more stylish.

On the other hand:

Ça a intérêt à être le bon bateau, cette fois.

and

Ça a intérêt à être un bon bateau, cette fois.

are still idiomatic but have different meanings.

The first one means “this better be the right boat”, i.e. the boat we should take to go where we want, the boat we are looking for while the second one means “this better be a good boat”, i.e. a comfortable, pleasant, reliable, etc. boat.

The choice between “le” and “un” is made depending on specificity:

• speaking of a specific item, use “le”,
• speaking of any such item, use “un”.

English offers the same distinction between “the” and “a”.

In the examples you have given, there are 3 different meanings of “bon”:

C’est dommage que bon nombre de photos …

In this case, “bon” is equivalent to “grand” and means large:

It’s a shame that a large number of photos …

Next:

Ça a intérêt à être le bon bateau, cette fois.

In this case, “bon” means right (by opposition to wrong):

It better be the right boat, this time.

Next:

Ça a intérêt à être un bon bateau, cette fois.

In this case, “bon” means good (by opposition to bad):

It better be a good boat, this time.

In the first and third case, the item is not specific, so you use “un” whereas in the second case the item is specific (the right boat) and therefore you use “le”.