Same Problem
Armbian uses log2ram for /var/log. And log2ram writes logs to storage every 1 hour. Basically if you install services and reboot computer before write all changes including new folders be missing
most easy option is for example:
sudo apt-get install apache2
sudo log2ram write
sudo reboot
and all works fine
for confirmation after restart run:
ls /var/log
and look for "apache2" folder
for chaking if system use log2ram type:
df -h