Hope nobody else runs into this problem, but just in case, we found the cause and a 'solution' for this problem:
The performance problems occurred because there was a table of the underlying MySQL database that LC uses to stores all content created in the Workbench which had more than 110.000 records and a size > 1.1Gb.
This is caused because the versioning that LC uses in de repository doesn't uses an history of changes between all different versions of the files in the repository, but always keeps a complete new copy in a the database.
After 2 years of template development this resulted in a huge table containing all these versions.
This is how we solved it:
1) make a backup of everything in the repository (drag&drop)
2) delete everything from repository
3) copy everything from backup back to repository
Even after deleting everything there still where about 42.000 records with old versions left in the database.
So if your creating a lot of template, fragments and other collateral in the repository keep in mind that at some time de database will grow extremely large and slow down workbench enormously with constant crashes.