Yes they can.
I've only been using it for a week or so but I've got a handful of home made markers and a few different multiple data point maps, some with different points using different markers. So you could conceivable pop each vendor's logo over their location ... or the corporate logo over the corp's offices / plants / customers ...
I followed the flash demo at www.bi4ce.com/documentation/dotnetnuke.map.html .
You specify the markers and their shadows In the markers section of the 'Interface' control in the map module's control panel. Check for my recent post about a marker editor bug. www.dotnetnuke.com/Community/Forums/tabid/795/forumid/130/threadid/226578/scope/posts/Default.aspx
I mention in there stuff pertaining to how the marker's parameters relate it to the actual marked postion. It's important if you want a tip or crosshairs some other demarcation of the point within the marker's graphics space.
Right now I'm playing with small datasets and small numbers of map markers. I have multiple maps with different sets of markers organized from the same pool of graphics files. Each marked point can specify any given marker in the set by index so you can have as many different markers as you want.
I started out making PNG markers but a friend's machine with IE6 was bletching those so I switched to transparent GIFs. They work fine ... I've even animated them :)
If you have graphics files you can display those in the popup balloon though mine are punching through the walls right now. I've only been at that part for two days tho and I'm sure there's info somewhere about how to properly specify the balloon's size. Other things like formatting and links work in them ok.