Hi,
Why are they missing? I'd be concerned if there are are other issues with the databases as well. However it is also possible to 'over index' a database whereby you can have a negative overall impact on performance. So for example you may create an index which improves lookup performance but has a negative impact when inserting the record into the database in the first place.
So yes go ahead and create indexes which you'd expect to be there but I'd be wary about doing anything more.
Cheers,
Mike