While we can use "a cloud of doubt" or "a shadow of doubt," these are more metaphorical expressions than specific collective nouns.
If you're looking for a word to describe a collection of doubts, you could use:
* A swarm of doubts (evokes a sense of uncertainty)
* A murmur of doubts (suggests a growing unease)
* A torrent of doubts (implies a strong and overwhelming feeling)
Ultimately, the best word will depend on the context and the specific nuance you want to convey.