I don't think HAM is interested in connection type. It works perfectly, no matter of connection type(e.g. 3G or WIFI). HAM will check for updates at the time that you have ran the gconftool command after the check interval had been reached.

is there any chance to disable auto update after every run of wlan connection?

Disable all the repositories.

When you would like to check for updates, enable the repositories that you want to check.

they should do sth with it, not only disableing repos

Try disabling all repos using HAM and use them as you wish with F-ApMan. This will prevent update alerts but still allow you to get new software.
NB If you do this apt-get may not work.

fapt-get will though

Is it necessary to run the gconftool command line or will editing the xml file suffice? I've tried the edit file method and found that checks were still done way too often (and 3G data usage remained high).

@chill,

Use gconftool.