You're attributing one thing - suspicion of a particular denomination - to something which it may not be related to. It may simply be due to how common a particular denomination is used in the cash economy.
In the Eurozone, €50 notes are very frequently used - it would be unusual to be specifically suspicious of that denomination - while €100 notes are far more rare.
To support this, I almost never see $50's. The dominant bill in the US is the $20, followed perhaps by $1, $5, $10, $100 in roughly that order. (that's my own estimation though)
You could be correct although I saw many other people paying for things with $50 notes too. I didn't think they were rare. Maybe it is store policy to do the counterfeit checks on $50/100 notes?
I can count on one hand how many times I've had a 50 in my wallet. We normally use 20s in the US. When I worked in retail policy was to check anything larger than a 20.
In the Eurozone, €50 notes are very frequently used - it would be unusual to be specifically suspicious of that denomination - while €100 notes are far more rare.