Technically if you're going to Azores you shouldn't have to "hop" via Lisbon, you should go directly to Azores since there's a huge airport there now. On a biased note, you should really go there, it's really gorgeous and the food is amazing! They cook a pot stew with volcanic heat that is just amazing, people line up from 5 and 6am just to keep a place in line.

I had the same experience that you had in Lisbon but I didn't had anything sensitive, just a couple of external hard drives, my laptop cooler and the respective cords inside my backpack.

Thanks again for all the help and I'll keep you all posted with my experiences when I do fly in a couple of weeks