I have to free up some disk space and I saw that Haiku keeps the binaries (already installed) packages in /system/packages (in my case it 17 gb of data). Is it safe to remove theese files? Its pretty dumb to keep the binary right there must just a sql database or simple text file that keeps the correcty version? Or?
As janus2, I assume you mean the “administrative” folder in /system/packages. It can be cleared out, but then you won’t be able to go back to past states by selecting one in the boot options.
A large number of states also slows down booting, so there’s a ticket (#12498) to remind us we need a solution.
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Just making sure… 
A naive reading of your post might suggest you are thinking of removing the contents of /system/packages itself.
DON’T DO THAT!
Your “installed” binaries actually reside nowhere but in those packages, and are unpacked as needed.
You probably knew that, and I’m misinterpreting, but just in case…
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I dont know if the script is running correctly on current nightlys, but to take a look this tutorials should be helpful:
http://old.besly.de/menu/search/archiv/pref/avoid-longer-boot-times_eng.html