In the specific case of slowing light with a Bose-Einstein condensate there will be a limit because the slowing of the light is due to an interaction of the light with the BEC to form a polariton. If you put too much energy in you'll destroy the BEC and it will stop slowing the light. Offhand I don't know what the limit is, but it will be a very small amount given that BECs need to be maintained at millikelvin temperatures.
More generally, there is no need to slow light to fit more light into a given space. Photons are bosons so there is no limit to the number you can put in the same quantum state. As Brandon says in his comment, ultimately the limit would be that enough energy in a small space will form a black hole. However this limit is many orders of magnitude above anything we're likely to achieve experimentally in the foreseeable future.