Summary:
Apache includes everything and the kitchen sink. Some of its features are bad for privacy and leaks info about a server's configuration:
https://mascherari.press/why-onionscan-should-worry-you/
https://mascherari.press/thwarting-identity-correlation-attacks/
Alternatives to Apache we can possibly recommend instead: Nginx, reverse proxies in general, anything very simple that's enough for most people.
Related Documentation:
https://www.whonix.org/wiki/Hidden_Services#Hidden_Webserver
ALPaCA defense
https://forums.whonix.org/t/website-fingerprinting-defenses-at-the-application-layer
?