For one, safety. There are some competent conversions out there using OEM parts, but many converters use surplus or merely re-weld parts.

Cosmetically, this means your dashboard may look slightly wrong.

Value-wise, you will never know if the instrument panel used in the conversion is the original. Original mileage and condition are very difficult to assess due to this.

Safety-wise, poorly welded conversions are outright dangerous due to the possibility of snapped linkages. For conversions done with surplus parts, the condition of the parts themselves might not be very good. Also, a fair amount of welding and re-mounting is also needed for these conversions, and workmanship may vary.

Also, JDM vehicles have headlights that are aimed wrong. The left lights are adjusted higher than the right ones, to highlight pedestrians on the left of the vehicle. In the Philippines, this means you are pointing your headlights straight into the eyes of oncoming motorists. JDM vehicles also have the smaller mirror on the right (a problem, as this makes the blind spot on the right side even larger) and passenger doors on the left (a safety hazard for your passengers, especially if you want to use the van as a commuter shuttle).

In the end, if you've taken care of all of these problems by getting a conversion from the most reliable shop you can find, and with original equipment, the last drawback is that you're killing local manufacturers and retailers. The local auto industry is worth about 1.4 billion pesos (unsure, but it's around there) and employs many Filipinos. By supporting imported secondhands, you're weakening an already poor local industrial base for carmakers.

This is the reason Toyota is already pulling out much of its capacity from the Philippines. Nissan's industrial presence here is small, and not growing. Thank god we're the local assemblers of their most popular product (the X-Trail) so they're not suffering much.

If you need to buy secondhand, buy local. It's less hassle. :D