Unplugged Wastegate Actuator?

One feed comes from the compressor housing on the turbo and the other from the inlet manifold. The one I would use would be the inlet manifold to be sure any boost drop through the intercooler would be allowed for. If you use the compressor housing feed then the plumbing will be short and tidy but 10psi at the turbo may not be 10psi at the inlet which means you could be robbing yourself of power. The factory designed it with two which means you should probably run both.

The blocked pipe usually goes to the Turbo Vacuum Switching Valve (T-VSV), which is basically an ECU controlled bleed valve. When its closed, the wastegate will see manifold pressure, and boost is limited to 7psi. When its opened, it vents a little bit of air, so the wastegate won't see 7psi until the manifold reaches about 10psi. Its how the ECU controls boost, based on knock or temp feedback.
If you plan to run a boost controller usually you'd block off the second connection. Don't want to raise the boost, and then have the ECU raise it even more.

Like I said I could be wrong. I just remember when I pulled my engine seeing that the hose coming from this sensor connected to a metal tube that then connected to this hose and it was cut in the center and both end blocked of with a screw. 
 
As for engine life. It wont do a thing; it is only a means for stock boost control. This becomes moot with a aftermarket boost controller so dont be concerned. 

There you go....mine was obviously hooked up wrong at some point. 
 
Here is a link showing the hose and explains why it gets capped off
http://www.turbomr2.com/MR2/HowTo/APEXI%20AVCR/Installing%20APEXi%20AVCR-02.htm