Are there any case of scam in such cases?
Its not unusual to pay a deposit in cash but the agent wanting her fee in cash is a bit odd in my opinion. I would tell her that you would prefer to pay it into the firm's bank account. Bank transfers are a common way of doing business in Poland. For the cash deposit you should request a receipt from the owner, dated and signed with his signature and his PESEL number and get the agent to stamp it with the company stamp.
If somebody runs off with your money you go to the police same as you would anywhere really. You should ask to see the owner's ID with his PESEL number. I would also want to see the confirmation of his ownership of the apartment. That would either be the print out from the Ksiega Wieczyste (that's the land and mortgage register where the owner's name is listed) or the notarial deed confirming his ownership.
It's very unusual to be scammed by a reputable agent but it's a business with a high turnover of staff and occasionally individuals go to work for these agencies and try to get a bit of cash on the side for themselves with a few dodgy practices. They get found out quite quickly and move on or are fired but the damage is done.
Here's an article you might find helpful. If it shows in Polish just use Google translate to read it.