As you mention - DB2 is not supported under Microsoft VSS. This means that Nimble cannot create database consistent snapshots either via the Microsoft VSS framework or through vCenter's snapshot mechanism (the latter uses VMtools & VSS within the Virtual Machine). Without utilising these frameworks, your snapshots will be what's called "crash consistent".
You can absolutely take crash consistent snapshots by utilising Nimble Snapshots & Collections. This will have no impact on your production database itself, but the databases themselves will be akin to having the database crash - ie some transactions may not be complete.
I personally recommend that all my customers (regardless of running Oracle, SQL, DB2 etc etc) to take crash-consistent snapshots throughout the day - reason being that application consistent requires the database (or VMs) to be paused to flush logs; meaning it could take seconds or minutes of time. You can still use those snapshots to clone and restore your databases very easily. In fact, Oracle fully support using crash consistent snapshots to restore back databases.
I hope the above helps. Let us know if you have any more questions.