It has been a while for Andrea. :)
symlinks
Nope, just create the addon domains within the hosting software and tell MT where to place the files. Almost same method as the original method of doing parked domains with mu.
The size of the codebase
*shrug* I don't see it as an issue myself.
perl
Only comes into play with rebuilds and saving the content. During regular page viewing, it's the static files. Perl doesn't come into play.
Blog count
Granted the enterprise version is a paid version with limits on the number of blogs but the open source version is free and it has no limit on blog or user quantity.
MT support
Just like wp, SixApart can serve as consultants. There's also community based forum support as well. Both for the Open Source and Paid versions.
Being honest though. Since you're doing this commercially, paid support is probably what you;re looking for. Most consultants for both platforms are 1 or 2 man operations. Automattic and SA are the big ones for both. Just wanted to throw that out there.
static files
MT has a php mode. You don't have to do it via a static site. You can even build a site with static files while including php includes for stuff like a Recent Posts list that can be updated without rebuilds. There are a couple of bugs though with them currently.
Templates
The ones that comes from the MT website and many of the ones available from the net are css based. You can modify the underlying code though via tags. MT does have widgets as well. Same general usage as wp and wpmu. You can modify them from within MT though while wp's widgets, you have to access the files via whatever server or hosting backend you;re using.
Centralized control
MT does have a backend that does do this but I have to admit that I like wpmu's better. Plugins and themes in MT are turned on sitewide, not just on a per blog like mu. Not sure about the Recent Posts and whatnot lists for MT.
Having said all that, the question that comes to my mind is who's going to use the site. If all of your writers are going to be in house, I'd lean more towards MT. If you're going to run more of a general site where anyone can sign up and create their own blogs, I'd lean more towards mu.
No matter what platform you use, you;re going to have to worry about maintenance and coding and upgrading and what not.
Hope this helps