The choice of grammatical tenses is fine except using until with the present perfect. However, there are other problems:
- vegetation is uncountable (see e.g. here) and so it can't be pluralized;
- rotten is an adjective; the past participle of the verb to rot is rotted (see e.g. here).
- eons just pass; there isn't something else that passes them.
- as far as I understand, bamboo wood is a particular manufactured modern material, plywood made of bamboo (see e.g here). What they would have used is thus just bamboo, not bamboo wood. (By the way, remember that bamboo is actually a grass, not a tree.)
- As user Weather Vane pointed out in the comments, we normally don't refer to boats as vehicles. Moreover, as user Jason Bassford pointed out, since it refers to boats, whichever word is used here should be pluralized (if countable).
Were they, for example, to build boats using available materials such as bamboo or other vegetation, the vessels would have rotted and degraded in a few decades, let alone the eons that passed until this exploration.
This is acceptable, but personally I still don't like the ending. I might prefer something like
… let alone the eons that have passed since then.
Moreover, depending on what exactly you are trying to say, you may want to a different tense at the beginning, as user FumbleFingers said. As it is, it sounds like they were making a decision based on what would happen to the boats in the centuries after they are built. Presumably, that's not what you actually mean. It is therefore probably better to use one of the following:
Had they, for example, built boats using…
Were they, for example, to have built boats using…