1a. Custom annotations in Chargeback data mart: To the best of my knowledge, custom annotations do not propagate beyond the Inventory data mart. To access them, you will need to use SQL to join tables from Capacity and Inventory.
1b. Custom annotations on FC Path in the Inventory mart: I don't think this is possible; Path does not seem to be an object to which annotations can be applied in the GUI. You will probably want to work out a way to record the necessary data in an annotation on either the host/vm or the volume.
2. What Matt said. Depending on what you're trying to do, it may be as simple as
select host.name, count(logical.id)
from host, logical
where host.id = logical.hostid
group by name
This will get you a count of the number of paths associated with each host. Where a volume is shared among hosts, it will be counted with each host. You may want to make sure that iSCSI and NFS are included or excluded in the manner you expect.
3. I do not know. If you figure out a process, please share! You may want to investigate Cognos triggers; a Google search for "cognos report trigger" turns up a few hopeful-looking results.
4. I don't have an HDS array in my current OCI environment, but if I recall correctly the string you need to put in the Exclude box appears in the Data Sources view, Devices micro-view, either Device or Originator column. Make sure you're getting it entered correctly. Once you have configured the exclusion, force acquisition on the data source and let it run to completion. Then return to the Data Sources, Devices micro-view, right-click on the line for the array you've excluded, and do "Inactivate Originator". If you're inactivating a large array, this will run for a long time. Let it finish. Then, assuming you do not intend to re-discover the array with another data source, go to the Storage Arrays view, right-click the array, and "Delete Inactive Device". Assuming all of that works (I'm reciting this from memory), please submit feedback on the KB article requesting that the more complete process be added.