I've been joining tabular and spatial data for 25 years now, and I still encounter challenges
with every new dataset, so yes there are likely to be issues, but it's difficult to predict what
they may be.
I'm confused as to what you might fear about deleting unneeded data with Catalog. As long
as you drop the tables using the highest level of registration (ArcGIS to delete tables registered
with the geodatabase, ArcGIS or ArcSDE to delete tables registered with ArcSDE, and ArcGIS,
ArcSDE, or SQL to drop unregistered tables), you're unlikely to corrupt your ArcSDE geodatabase.
I don't use ArcCatalog all that often, but when I do, it's usually to export data from ArcSDE;
I don't understand how this could be a bad idea.
- V