I have set the option

hackablelockedcrate.requiredhackseconds "120"​

in console, when connected to my server. Afterwards I've executed

server.writecfg​

 and there is no 'hackablelockedcrate.requiredhackseconds' in ../server/serveridentity/cfg/serverauto.cfg.
So I've added it manualy and restarted a server. When server was up - i got 15 minutes (default value) timer again.
What am I missing?

If I understand correctly, on server shutdown

server.writecfg​​

executed, so my changes are gone. How can I prevent this, or how can I get changes saved?

put this

hackablelockedcrate.requiredhackseconds "120"​

into the server.cfg

You'd want to use server.cfg, not serverauto.cfg. Using server.writecfg / writecfg will have no effect on either of those files as it is only for bans and users.