Once a train reservation load hits an upper threshold, they can be disabled automatically.
Similarly, if people buy the fixed upgrades via Seatfrog or a secret price bid wins, that can end the auction and eliminate availability far earlier.
If a train is suspected to be disrupted or problematic, they can be manually withdrawn too, e.g. during bad weather. Can happen when there's a shortage of staff or catering supplies and the first class offering may be reduced.
Some trains are now permanently unavailable simply because the yield management strategy for that service calculates more money can be made without selling a Seatfrog upgrade, particularly peak time services popular with business passengers.