I have a 1998 VX 3.4L petrol Prado and earlier this year added the snorkel. I noticed a improvement in highway driving and a slight change to the economy and power. The big thing is clean cool air is being scooped into the engine instead of from the wheel arch plus the intake is over 600mm higher in water conditions. Being a petrol you still don't want the engine that deep in water.
Things I found to improve the Prado are:
Clean the MAS (Mass Air-Flow Sensor)
I changed my spark plugs to Bosch Platinum’s (FR8HPX)
Clean the fuel injectors
Here is the thread about it http://www.4x4earth.com.au/forum/my-4wd/4274-toyota-prado-90-series-1998-a.html
I personally believe the cost of the snorkel is worth it but look at it a as cheap insurance while driving around water.