A motivated competitor has the legal right to reverse engineer your product -- you do need to protect yourself.
A patent would be nice, but often a patent is too expensive, and that may not deter a competitor.
If using Virtex II, IIP, 4, or 5, I suggest the lithium coin cell battery from Ray-O-Vac, and the use of encryption. That is a minium of
15 years of battery life (to 2.0 volts), and since the key is maintained down to less than 1 volt, Ray-O-Vac is unable to extrapolate the lifetime beyond their 2 volt end of life (they said "as close to forever as you can get"). As long as their is reactive lithium in the cell, it is able to push out electrons.
Set top boxes use the lithium battery solution for example (they know how to protect themselves).
If using Spartan, there is no comparable encryption solution.
Some customers use the 3AN (with internal prom) as they feel that has sufficient barriers to reverse engineer (no signal of the configuration appears externally).
Identifying a small part of the design, and reverse engineering just that part is tough, but not unheard of.
The other choice is to hide, or obscure the design as best you can: I know that the crypto community chants "there is no security in obscurity" but obscurity is used by most anyways (causes the thief to look for something easier).
Obscurity is the solution favored by natural evolution (so it does work well enough ...).