That's possible, but if that's the case, then why haven't the project managers put all this speculation to rest? Why all the spooky hush-hush secrecy?
Any project this large has one or more people on the payroll whose sole function is to talk to the press. The only statements we've heard from the project principals, is that they've encountered something "unknown", and that boring has stopped until they can determine what it is.
If the situation is what you suggest, it seems they would have indicated that from the very first. In fact, it probably wouldn't have even been newsworthy.
They haven't been able to look at it yet. Water is flooding in both from the Sound and from landside. Not just water but high-pressure water. Adding pumps. No conspiracy.
That's because they don't want to admit that they drilled into the foundation of the "Space Needle".