Hedde,
The UUID's will be imported identically to the exported components. I can't think of any reason why having identical UUID's on a separate system would be an issue.
If you wanted to change their UUID after importing them, you could clone the object and delete the original.
One thing to keep in mind when importing/exporting is that while index schema configuration and query settings are preserved, shard settings are not attached to the individual index, they are attached to the Index service, and are not preserved through import/export. You will need to create a new Index with the proper shard configuration and attach it to your imported workflows.
Hope this helps,
-Jared