Personally, I would swap in a JDM ECU if running without the EGR. The differences in the open loop operation may be significant enough to have a decent effect on longevity... over a couple years I wouldn't expect to see much but over the next 20, maybe. The difference in the EGT (Exhaust Gas Temperature) on a USDM with EGR and then with it removed (but still running the USDM ECU) are vastly different; I've seen studies with logs showing anything from 50°F up to 200°F in increased exhaust gas temperatures (not Supra specific, but it should serve as ample warning)... think about how much hotter it is in the cylinder when you reach the hottest part of the burn.
On most newer vehicles which monitor EGT it is usually required that you remove or recalibrate the EGT sensor to present the ECU with false readings which match the specified. This is done by either replacing the sensor with a specific value of resistor, adding a resistor in series with the sensor (if the sensor uses a NTC type thermistor) or the replacement with an alternate sensor which operates on a different scale (necessary with PTC type sensors). Older vehicles the resistor replacement is usually fine as the ECU doesn't care if the signal is static; newer vehicle ECUs often check the readings of the sensor against an actual table in which case simply swapping in a resistor is not an option. These sensor readings are used to determine the best adjustments for cooler temperatures with minimal power loss.
Many newer vehicles *appear* not use EGR systems. This is due to new methods of introducing those same inert gasses and better ways of controlling them such as monitoring exhaust temps and using variable valve timing to allow exhaust to flow back into or remain in the cylinder on the exhaust stroke or immediately thereafter... and guess what, newer JDM vehicles do employ these methods (probably more due to economy benefits than emissions but they both go hand in hand here).
Now don't get me wrong... I don't care at all if anyone wants to remove it or disable it; I just want them to know all the angles before they do and make sure people aren't just telling them to get rid of it just because "everyone else is doing it" or "that dragster don't got it". 
If you feel the need to advocate a change to someone else's vehicle (and no, no one in this thread was doing so) it's only right you give them the full details, especially when the side effects could be detrimental.