Its a nice script, I have a question wont scheduled Index Maintenance plans have the effect of showing up in the last_user_update?

You could also change the nested CTE to simply be

Select db_name(database_id),Max(x.Last_Date) Last_Access_time

From

sys.dm_db_index_usage_stats

CROSS APPLY(VALUES(last_user_update),(last_user_lookup),(last_user_scan),(last_user_seek)) x (last_date)

Where last_date is NOT NULL

AND db_name(database_id) not in ('msdb','master','tempdb')

group by database_id

Drop that into a single CTE for use as the source for the merge and you should be good to go, all you then have to do is the date diff on the merge.

I would also look at adding a clause to the WHEN MATCHED to only update those rows where the Last_Access_Time is different

So the code reads

;With Cte_Src(

Select

db_name(database_id) databasename

,Max(x.Last_Date) Last_Access_time

,GETDATE() curr_time

From

sys.dm_db_index_usage_stats

CROSS APPLY(VALUES(last_user_update)

,(last_user_lookup)

,(last_user_scan)

,(last_user_seek)) x (last_date)

Where last_date is NOT NULL

AND db_name(database_id) not in ('msdb','master','tempdb')

group by database_id

)

MERGE master..AuditTable AS tgt

USING Cte_Src AS src

ON tgt.databasename = src.databasename

WHEN MATCHED AND src.Last_Access_time != tgt.Last_Access_time

THEN

UPDATE SET

tgt.last_access_time = src.last_access_time

, tgt.no_of_days = DateDiff(d,src.last_access_time, src.curr_time)

, tgt.last_upd_dtm = src.curr_time

WHEN NOT MATCHED BY TARGET

THEN

INSERT (DatabaseName,last_access_time,no_of_days,last_upd_dtm)

VALUES ( src.DatabaseName,src.last_access_time,DateDiff(d,src.last_access_time, src.curr_time));

It needs testing.

One last thing user objects should not be in the Master DB, I would create a centralised Audit Database or a specialised DBA database on each server to hold this type of thing as all you are doing is clutering up the Master DB.

(code reformated)