It seems that whatever is down there wasn't meant to be dug back up. Burying something that deep with boobytraps seems like it was meant to be a permanent resting place, so to speak. So, what kind of "treasure" would be buried where it could not be retrieved?
I've given a lot of thought to this over the years as well. My feeling has always been that the main shaft, the Money Pit itself, was designed so that if anyone did find it, they of course would eventually run into the flood tunnels and not be able to retrieve what is down there. By the same token, I believe that whoever did this, may have designed a secondary method of being able to retrieve the treasure themselves, by digging down through virgin ground that used surface markers to indicate where the treasure was at. In other words, I feel that lateral tunneling was done by the originators of the project, in order to have a way to get to what they buried.
Although a large part of me still thinks that Spanish conquistadors, using slave labor, are responsible, I have to admit that the Templar theory is becoming even more plausible to me. I would really like to know where Zena's map was found, or if the paper itself has been examined and dated. If real, it predates Henry Sinclair's trip by at least a century or more (Sinclair may have come to Nova Scotia in 1398).
But you are definitely right, it seems that whatever is there, was meant to stay there. Time will tell.