If they can transport tons of cocaine, I am quite sure the drug cartels will find a way to transport double the weight in money. Getting rid of the $100 bill won't deter crime. The gov't tells you that so they can justify their actions and create more demand for their services. Every time they change something - currency, ID requirements etc., it is billions of dollars of control, legislation, implementation, favours owed etc. as it gets enacted.
If hookers only accepted $20 bills and not $50s or $100s, I would still hobby just the same.
If a crime gang can figure out how to manufacture, harvest, import and disrtribute a prohibited drug, I am quite sure they will be able to figure out how to get paid in $50 bills instead of $100 bills.