I think it's a load of factors repeatedly adding up to a larger number.
1. Higher ticket prices have slowly turned away a load of otherwise die-hard fans
2. Ticket policies have made it increasingly difficult to just pass your ticket onto a mate if you can't go
3. We play more home games than any team outside London and it adds up financially, so people pick and choose
4. Travel options to and from the ground aren't up to standard for quickly moving 50,000 people
5. Season ticket holders not coming to cup games and not selling their ticket back to City
6. Large batches of seats being withheld by City and sold to tourists on Viagogo
7. City fans saving their money for bigger games than (what was essentially) a dead rubber before another Wembley trip
8. At least 4-5,000 are generally missing from midweek night games in the cup (always been this way)
If each of the items in the list affect, say, 1,000 people, then you're gonna be down at 44,000 anyway.