I assume you are talking about this one: http://rib.net/forum/showthread.php?p=323852#post323852
I'm not sure they are holes? It would be worth asking the vendor for info about them and photos if they are holes/screws etc. Perhaps something was left on the deck and has stained it?
I'm not an expert on Seariders but from what I know 4.7s are quite rare so do attract a premium. Its probably hard for people to comment on the value without knowing more about the engine hours (its 11yrs old so could well have had a hard life) and the age of the boat. Then I guess things like the possible deck holes, patch on the tube and gelcoat patching probably require personal examination to make sure your not buying a pile of headaches.