I have to say that i can clearly remember seeing the matte boxes in the cinemas back in '77. Back then i knew nothing about special effects and the way they were done so we all thought that they were the ships shields. I remember they were more noticeable during the Falcons escape from the Death Star. I use to do a lot of drawings back when i was kid and from '77 they were mainly Star Wars related. I actually drew the TIE fighters with these boxes around them many times because that's how i thought they were supposed to look.
As for the restoration i don't think they should use digital compositing for any of the effects shots. Everything should look as it did when the films were released. The effects in Star Wars were ground-breaking and this is part of cinematic history and thus should be preserved accurately. Generations should be able to see how these effects were achieved and how they attempted to overcome the limitations faced at this time ( transparent ships etc). Recomposing any effects using todays digital technology would not be a true preservation and i would be totally against it.
I hear it so many times from people who are new to the saga saying how amazed some of the effects look for a 1970's movie, but they are actually talking about some of the CG/ re-composited effects thanks to the Special editions. This is NOT what we should be allowing new generations to believe. Clean up the films - yes. digitally remove all the dirt and scratches - yes, because these faults were not part of the original movie but down to the passage of time/ useage. But change anything else like removing the matte boxes / matte lines - hell no.