First of all, the servers do require assets from a client install in order to serve the maps, etc. While the project may have been coded from the ground up, there's still that attachment and use of EA's copyrighted content.
Open Office, Libre Office, Bean, and other word processing software is able to read, write, and make use of Microsoft Offices proprietary file formats, show me a difference?
Secondly, if I installed UO to a machine without every starting an account, ie. I never even did a click through of the EULA/ToS how would it apply? Third you'd have to prove I accepted the EULA/ToS first for any of that to matter. Fourth UO doesn't use proprietary File formats for it's animation or map files, this means I can create any type of program to read them and there's not anything EA can do about it outside it's own network, the servers are not altering, modifying or redistributing them, the server operators doesn't view them anymore than me or you do, at most the server software indexs them as a reference. The software is just reading them and that isn't illegal, if it was every Antivirus program on the market would be illegal.
Don't get me wrong, I'm not in favor of people playing on Freeshards, quite the opposite. But there are many applications in which the use of EA's property is legal, such as to show criticism through satirical videos and teaching.
If someone make a satirical UO Video comic to show their displeasure of the state of the game using an emulator, that's protected. If I was to use it to teach lessons in basic economics, as an educator that could be considered protected.
Everyone attacks freeshards on the concept of "It takes people away from UO" and that I can agree with, but I'm also going to argue on the merit of that there are other positions where Freeshards can be used in a beneficial manner.
Here's the biggest problem, the Emulator Software is legal, it's how people use it that throws it into a possible conflict, it won't even run unless someone modifies it to point it at files in the UO Clients install directory. Saying the Emulator Software itself is a violation of any laws is wrong, it's how it's used that should be called into question, you can't attack the emulator you have to attack the individuals who run it.
Can EA shut down Freeshards, maybe, it would be difficult there are a ton of things EA would have to prove first. UO is the only MMO I've ever played you didn't click through a EULA when you go to log in, and again after every major update. EA cannot prove anyone of us has physically clicked that button saying "I accept", how many folks have given accounts to family, or friends? How many of us have every paid for a family members account? I can't force someone else into a contract that's illegal itself.
If a person installs and uses UO with out ever having the intention to play on EA's service and never sets up an account or registers a disks [Account Key] how can the be bound by an agreement they were never presented? UO has some major flaws when it comes to protecting it's rights inheriant in it's design.