I could be mistaken here but:

Mask is a metal layer which would be vulnerable to a physical inspection
of the part (after peeling away the plastic with nitric acid).

OTP EPROM, Flash and other field programmable parts are programmed by
burying a charge (much harder to get a look at that!)

Microprobes would probably allow a sufficiently motivated organization
to hack your code but the act of getting the probes to the die would
probably disturb your code.  Much harder to get to the die in a plastic
part than a windowed part.

A few years ago people were trying to use electron microscope techniques
to detect voltage levels in circuits but at the time these methods were
not very fast.

mink