Two reasons I have read is that the larger bills are counterfeited more often and some robberies have used large bills to get managers out of the office to make change and then proceed to rob the place.
I used to work in a bank and we found more fake $20s than $100s. The counterfeit pen doesn’t work because they take $1s and $5s and bleach them, then reprint the larger denomination on it. Most people don’t know exactly what to look for when examining currency to determine if it’s counterfeit or not.