A lot of agencies nowadays go by the form deposits and some may not even meet them in person and only go by feedback/complaints from punters. If they are reputable, then they do care and if not, then they let it slide until word gets around and punters gradually stop using them.
There are definitely pros/cons of both working for agency and being independent. Agency girls are expected to work nearly 24/7 unlike indies that set their own times/days etc. Agencies don't like part time WGs as its in their interest to make as much commission as possible and a part-time girl won't fit the bill.
Also, by some accounts, they no longer get involved in finding flats for their girls which means no incall flat = not interested, so there can be some dumps even amongst agency girls.