We use Eddy Current sensors extensively, with substantial accuracy. It is not cheap but it is the most consistent, predictable way of doing it. We are currently using it, among other things, to probe a hole that is approximately .150" diameter. Not only can we tell whether or not there is a thread, we can tell with some certainty the quality of the thread. i.e. whether or not the tap ripped any threads, if the tap went deep enough or too deep as well as some other things.
I believe that there are a few companies offering Eddy current inspection equipment in all different states of assembly from component to turn-key solutions. We have been dealing with SE Systems in Califonia.
Here is his contact information:
Geoff King
SE Systems, Inc
(510) 723-6006 (V)
(510) 784-0810 (F)
I believe they have a website as well.
A.J.