I changed the theme to default, turned off all the plugins, changed all the mysql tables to to innodb and followed the recommendations of mysqltuner (even though, as I said, there's nothing about slow mysql in the logs I can see).
Changing tables to innodb causes mysql to use more ram so that the performance can decrease on low memory systems.
So why would an old, non-optimized app manage to query a 26mb database and parse a complex page in 0.119s, while Wordpress admin takes 6-9 seconds to load a 2mb db?
You compare apples with pies here. Not every mysql query is the same and the raw database size is only one of several parameters that affects mysql performance. If a query is slow or fast depends on a lot of things like joins, if it has good indexes set and if the temp table has to be created on the harddisk etc.
One indicator for low harddisk performance is e.g. when you run:
and the results are slow, rkhunter searches trough a lot of files, so if its slow, then your harddisk performance is low.
One other thing that you might want to check is if the nameservers in /etc/resolv.conf are rechable and responding fast.