How long does he can't play football? definitely is wrong.
How long can't he play football? It doesn't seem to be wrong, but it feels weird. Maybe it's because we use can/can't to express ability and "how long can't..." implies losing ability for a defined period of time. Even thinking about a model situation is frustrating.
Here are some workarounds for you:
How long before .... can ... ?
How long is/are ... unable to ....?
hope this helps.