Subclipse does not write anything, Subversion does it. Subclipse calls the Subversion API, merge in this case, and Subversion does the rest.
Because you cannot select /trunk in Subclipse, unless you have checked out out separately a a project in your workspace, there is no way to write to it.
If you have 30 projects, I would do the merge using TortoiseSVN and then just do a Refresh in Eclipse to work with the results. Although you also would need to commit from TortoiseSVN in order to have /trunk included in the commit.
Subclipse has to do 30 separate merge "commands", one for each project. And each project will have the mergeinfo property written to its root. Subversion can handle this, but obviously if you have other content in /trunk that you want to merge, then you probably ought to either have that in Eclipse, or do the merge with another client.
Note that when I say Subversion handles this, what I mean is if you first do the merge in Subclipse and commit etc. Then later come along and do a merge at /trunk level using TortoiseSVN, SVN is smart enough to only merge what has not already been merged. It will also typically "elide" the mergeinfo from the 30 project roots up to the /trunk folder level.