In one of Bill Sweetman's book, all shots of the front were blackened at the intake for security reasons (which he pointed out). I can't seem to find any decent pictures of the actual intake online so I think it's safe to assume they were doing something.
Presumably they wouldn't give that info to the artist and remove it for museum duty, whatever it was.
"A visitor from Mars could easily pick out the civilized nations. They have the best implements of war."
I tried to get a better look at one of the photos using digital enhancement techniques (sharpen, contrast and brightness). Even with that, it's pretty hard to tell what's in there. However, I could see that something was in there blocking the engine face.
If I'm straying too far on the side of OPSEC, feel free to lock this, mods.
I'm guessing it's because they had to keep the engine so far forward in the aircraft, since they were using a direct gas lift system. There just wasn't enough room ahead of the engine face for duct shenanigans. Same reason the Harrier looks so... rotund.