Just noticed that the shield generator is placed in the Rough terrain hex. Does it mean that it gives a permanent -1 dice penalty when fired upon?
You are correct. Here's what the rulebook says...
Destroying the Shield Generator
The Shield Generator is destroyed in the same way as a unit. It has an armor strength of 3, and if hit, it is destroyed. (Note that it is in rough terrain, and it does benefit from being there.)