When we are recovering from disruption we will use a number of approaches depending on the situation to get trains running as normal as soon as we can. As you point out, this can include some trains missing stops to prevent queues building (and also to make sure the trains next journey runs on time), or turning some trains around before their booked destination to save 20 minutes, etc on that particular round journey. There is a short video which explains our options here.
We always try to tell people what's happening to the best of our ability, as we agree that the more information people have the better. We are looking at various ways to imrpove this information, including both new processes and new systems (such as a new website and an improved customer information system).
We'll keep everyone posted on these developments, and trust that in the coming months everyone will see improvements in the consistency and level of information they get during disruption.