Bloopa,
The Alert regarding the Index state in the health report is not related to Deduplication, but to the index of protected files contained in backups. It appears based on the message in the alert that there may be a problem either with the Index itself or the SQL processes related to the Index on the CommServe. Unfortunately this is a much more complicated issue than can be reasonably addressed on the forum, and I would recommend opening a ticket with the customer support team. Please make sure to include an upload of the log files from the Index Server to help us in identifying the problem with the index.
As regards your Database Fragmentation, there are a lot of possible causes for the fragmentation, and expanding that report tile can help to identify the problem tables which are being fragmented. It is possible given your specific environment that we can expect significant activity on specific tables which may cause rapid fragmentation. Since the last DB Maintenance was run almost two months ago, we would also recommend running a dbmaintenance -recommended to reduce the fragmentation, and suggest scheduling the DBMaintenance Wiorkflow to run a recommended maintenance every 1 to 2 months.