The deposit arrived in 1999. And that's why we've had I think one new entrant since then that has managed to stick (and I reckon even that is only temporary). For instance the Phoenix team flew to the Malaysian GP in 2002 with actual cars and the FIA barred them because they had not paid the $48m deposit. So you have an instance there of the bond actively preventing a team that was ready, willing, and able to race.
I am not sure that's a good example. Wasn't Phoenix just another scam by Tom Walkinshaw after he basically ran out of money to run Arrows properly? It's been 20 years but IIRC, newly created Phoenix (headed by an old buddy of Tom W.) bought some remaining parts from the Prost fire sale, cobbled them together with parts from the Arrows three seater cars and tried to start and park under the Prost entry license so they could get prize money owed to Prost GP to finance his drowning Arrows team.
The FIA quickly shut that scheme down and Phoenix never raced and Arrows collapsed soon after.