Bert Kassies says this:
A licence is obligatory for clubs qualifying for UEFA club competitions in the 2004/05 season. A club which has qualified on the basis of sporting criteria but is not allowed to enter the competition because it has not obtained a licence, will be replaced by a club nominated by the national association on the basis of the rankings in the top domestic league championship (or by the runners-up of the domestic cup competition if the cup winners need to be replaced).
There's two precedents I can think of where clubs qualified on sporting criteria missed out on Europe, Slovenia 2003/04 season where 6th placed Primorje got into the UEFA and 7th placed Domzale got into the UEFA (this in a 12 team league) as only the champions Gorica and cup winners Maribor (3rd place) were able to secure a licence. I know Olimpija failed on the basis of money owed to players.
In 2004/05 no Kazakhstan club got a licence so none got into Europe.