"I feel that those with holes are just old stock paper left over from when cel were used for animation."
Animators still use registration pegs...easiest way to make sure everything is aligned, and it keeps the pages from moving while drawing corrections or in-betweens--one less thing to worry about.
As for cropping: The copy layouts that I have are cropped so the animators could tape on usable registration holes.
http://conri.rubberslug.com/gallery/inv_info.asp?ItemID=179201
I also have a number of sketches where the registration holes were cut off and realigned before being taped back on. This is usually much easier and faster than redrawing the image.
http://img.photobucket.com/albums/v727/conri/stuff/productionartwork/ep01natsukiduran07.jpg
You can somewhat see this in action with the three rough genga I have in sequence from this cut (115 KB GIF):
http://conri.rubberslug.com/gallery/inv_info.asp?ItemID=136035
I have yet to own a sketch, layout, or copy layout missing registration holes, but some of my sketches with realigned registration holes are taped on in such a flimsy way, I wouldn't be surprised if some get torn off or even fall off. Also, compared to genga, shuusei (correction sketches) and douga, I can't think that it is as imporant for layouts to have registration holes. Single cuts can have multiple layouts...The following original layout also has a copy background layout where the animators didn't bother to crop to tape on reg. holes.
http://conri.rubberslug.com/gallery/inv_info.asp?ItemID=179205 I've only really made note of one instance where a cropped rough genga without taped registration holes was being sold along with a bunch of uncropped genga, though I have wondered about a few auctions on eBay. I know with cels, some sellers like to leave out the reg. holes because it is more 'attractive,' but it is one of a handful of (non-foolproof) ways you can try to use to verify that something is actually production.
Personally, I'd be suspicious of an auction where all of the sketches were missing registration holes (especially genga, shuusei and douga), but since yours is the layouts which come with uncropped genga and douga, I don't see any problem.
[quote]I do know though that my layouts were actually cut because there's little jagged pieces along the top because they weren't cut cleanly. So if the scanners don't have the means to accomodate the registration holes, then it would make sense to trim them off.[/quote]
While layouts could potentially be scanned (I have instances from One Piece where rough genga were scanned, printed out, and eventually used to draw on the blank side), they aren't the ones that get computer colored (that would be the douga). Given the sheer volume of douga studios have to scan, their scanners have to accomodate regular-sized animation paper with registration holes. If they did have to cut all the holes off before scanning, I'd think they'd at least use a machine to help out. :D
Of course, studios are surely looking into ways of cutting the douga step [like they did the cel step] so they can save even more money...