Mike sorry I took a while to get back to these questions.
1. What kind of main lug amperage could be encountered in these panels,
2. Is there a main disconnect of some sort located in this electric room (or somewhere nearby),
I do not know how to perform arc fault calculations but what I do know of them it would be high. This store has it's own 13 KV to 480 V pad mount transformer located outside as close to the main disconnect in this electric room as possible. It is not more than 50' of conductor from that transformer to the lugs of the main. From what I understand this will provide one heck of a flash.
The Main disconnect is located in this electric room in picture one you can see the main gear on the extreme right side of the picture.
Typically for these stores it is 1,200 to 1,600 amps @ 480, I did not check the rating of the service in this particular store. The one good point is it has GFP protection.
3. Referring to the first picture, what is going on in the very large panel across the aisle from the SqD add-on panel? It looks like it's "taped up" also.
I could not get a good picture of that section but it looks the same as the gear in pictures 4 and 5. It is fusible disconnect gear being partly modified to breakers.
I agree with Pierre this is a total lack of pride in the work.
I also maintain that there are some truly dangerous issues in here.
Not to say we are perfect either, one of our service guys went on a service call to a building that the construction guys are remodeling. The service guy took photos and gave them to our safety officer. The job Foreman and the PM got their rear side chewed off for what showed in the pictures and it was nothing like the mess in my photos.