I think you've misunderstood me. There must be an underlying fares database which they search from for a given valid journey.
Retailers import fares data daily from an RDG source. Each retailer will then handle that data in their own way, but I imagine all will create a database of sorts, yes.
Why would that database not have every possible fare for that valid journey
Some fares are restricted in terms of the ways they can be sold, e.g. whether they are only available through one specific TOC's own website, TOCs in general, ticket offices etc.
There may also be issues with the way that a journey planner is able to interpret and thus offer the fare, especially if it's set up in a non-standard way.
and why do some journey planners identify fare options that others don't?
It would be best if you can provide us with an example of what you're thinking of, but in general terms it could be that it isn't finding (or is filtering out) a journey which the fare you want is valid on (e.g. one which is overtaken and/or which has additional changes).
It could also just be a bug on the retailer's end.
Does that imply that there are several different fares databases which differing journey planners utilise, or do different journey planners apply differing filters as to which possible fares to rule in/out?
They definitely apply different filters in terms of the journeys they show, for example TrainSplit and Railsmartr are good at finding cheaper overtaken journeys whilst most journey planners only show the fastest options.
For a given journey, the available fares should normally be the same across all retailers, subject to the above provisos.