Long queue is not related to any COVID issues. It's simply a function of:
1. Large number of non-EU arrivals (Lisbon gets a lot of visitors from Brasil in addition to US)
2. Relatively slow immigration processing (as a function of some of the visitors being subject to more scrutiny)
3. Relatively low number of immigration officers dedicated to non-EU arrivals (they have a total of may be 8 lanes physically available, of which not all will be non-EU)

I don't see how this situation can be much improved unless these factors drastically change.