I'm not specifically familiar with uninstalling MerchantE, but there are a couple risks inherent in uninstalling any bundle:
1. There may be custom fields associated with that bundle you're populating, not realizing they're associated with that bundle
2. There may be scripts/workflows/forms associated with the bundle that you're using or they're causing behavior that users are used to
If you uninstall the bundle, everything associated with it goes away, including data in those fields and stuff you may be using that you don't realize is linked to that bundle.
I'd recommend uninstalling in a Sandbox first and making sure you're not losing anything you're not expecting. And thoroughly analyzing the bundle components for the same reason.
All that to say....MerchantE is probably unlikely to have tons of custom fields and scripts compared to other bundles, so probably lower risk. If you were uninstalling something like Contract Renewals, I'd be more concerned since that installs approximately 10,000 fields, scripts and god knows what else.