I'm not sure what those are though it seems to have something to do with apache 2 as I have them on my Debian box and if I search for "?C=D,O=A" in Google I mostly get a list of file servers and mirrors.
As far as using Apache for a package repository their shouldn't be any problem with that. When you are serving the package through HTTP you should be able to use any web server. LANDesk just tries to hit the URL.
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Looks like it is the apache module mod_autoindex. It makes it so the sorting oder can be changed by specifying different parameters. Not sure why they show up though, I thought you had to type them in by hand.
This may be how to disable it: