It is not extremely rare to have a long queue for secondary checks, IMO.
The line at AK on Sunday afternoon (3pm) was 25 people deep with ONE CM doing the checking, and he was unloading every single bag. They set up a queue and it was beyond that. I see it often (we are at a park weekly), but it ebbs and flows with staffing and crowds. We have been caught in a 10-15 minute delay on several occasions.
I have also experienced rude CM's at the security check, and there is one that is notorious at Epcot (many, many, many posts about it in the Disney social media world).
Due to the increase in secondary checks here lately, we have really slimmed down what we bring into the park. I will 100% always be in favor of checks, even if we have to go back to individual bag checks, but wish it was better staffed/better trained/more efficient on some days. I have seen and experienced it done very well so I know they are capable