Blocking the EGR won't increase the amount of vibration made by the engine. It's a diesel, it's going to shake the shit out of everything anyway. Handy if you recycle toilet paper, not so handy if you're having to replace fragile pipes. Have heard of a couple of Navara owners with cracked EGR tubes, but I'm pretty sure those ones cracked on the exhaust side, not the intake side (it's hotter over there, so the metal is treated even worse).
Personally I wouldn't worry. Mine's been blocked for ages now - I did mine before the car saw 27,000km and she's done nearly 126,000km now and still purrs.