Since the launch of the DS server, we have blocked or moderated 400+ multiple account registrations. This is purely for Dragon Saga alone, and does not account for the full 2000+ reports we have had in the last year. Dealing with those reports takes quite a while as you have to do each one case by case, and it can take anywhere from 5 minutes to 20 minutes, and if I have to contact each person which then we give them several weeks before we take action on the report.
Also you are ignoring one key factor about multiclienting: account sharing. We can stop people from registering new accounts, and moderate or ban any secondary account registered but it becomes harder when they are using someone else's account. Because it is done at the game level, and not forum level, moderating and monitoring things are more difficult. It is also harder to step in and punish players for sharing accounts without being seen as excessive or overly restrictive.
Engagement
This is a problem in any game, but is less an issue of account sharing and more that farming is normally done solo except for harder end game content. If someone is going to run the same dungeons for 8+ hours, they are normally not going to do it with someone else, they are going to do it solo.
For the most part, only Paris and Elga really ever had the experience you are talking about where a group of people would grind it together repeatedly; most other content was done solo, or was done with account sharing.
Character Progression & Economy
Again, account sharing played an impact here, and it is not something that can reasonably be prevented without over moderation or a lot of oversight. If anything, not allowing two accounts would have been more harmful and would have created more of an unfair advantage for people who account shared.
As far as PvP goes, we have plans for introducing some monitoring for this, as it is one of the few areas where multiclienting abuse really does have a harmful impact.
In our own content, we would look at doing mechanics that are harder to deal with when multiclienting in dungeons.