Maybe teams were not well organized because they had trouble organizing stuff around taking part in WNL...
And if you only fight two scrims a week when you're taking part in two competitions it means you're not doing any practise scrims.
EDIT: You're also not considering the fact that the 5-a-side team and WNL team might not consist of the same members.
EDIT 2: Regarding your edit, that is exactly when you will see problems, because different clans will have different schedules, making it harder for you to schedule your 5-a-side matches.