I think that is the same boats we saw in Season 3 when they left the Hydra after Ben's surgery to return to the main island. So I think they have been there the whole time. I knew those boats looked familiar. So I am guessing Ben knew they would be there, but the runway is the question, how did they know it would be needed.
The year is 2007 for Sun, Ben and co. At the beginning of the show, they flashed back 30 years. Ben's surgery was late 2004 and I am guessing no one was back to the hydra after 2004 including the mercenaries. So I am guessing Ben always knew they were there.
It's worth it for Ben to check it out, if he knew they were there when he left in 2004/5. If they were there when the others moved of Hydra Island after his surgery, then why wouldn't they be there in 2007/8? No one's gone back to that island, that we've seen, in that time between when the FDW was turned and now.
The palm fronds did look fresh though, but I can chalk that up to a small oversight and be satisfied.
Just a thought....Maybe 2007 Ben is getting NEW memories on the little island from 1977 Ben? Like Des got the new memory from Dan? I know in Namaste we just saw Ben meet Sayid but who really knows what that KId knows in 1977, I think by now he is working for the Hostiles (Richard) and may know a lot. Little Ben may be giving Big Ben new memories.