Poor weather can disorganise an airline's operations.
However the compensation is still payable. It is entirely under the airline's control HOW they handle any weather disruption. For example, British Airways, as a matter of policy, if there is any disruption, cancel many of the domestic sectors at Heathrow while still ensuring they get their full long-haul programme away in the limited slots available. It is entirely a commercial decision to do this, which flights to delay/cancel when there is any shortage of resources. There is no reason why cancelled passengers should suffer from a "some passengers are more important than others" policy.
Likewise if there has been poor weather it is wholly the airline's commercial decision the extent to which they hold reserve capacity of standby aircraft/crews, or not. If they choose not to, or run out, that again has been a commercial decision of theirs.
Carriers typically know the percentages of flight losses due to disorganisation they encounter over the year where they are liable to compensate passengers, and the regulators expect them to build these numbers into their overall cost of doing business.