Set an alias for the herbstclient command in the autostart script that only stores its arguments and executes them all at once at the end of the autostart script.
This reduces the amount of flickering you get while all options are being applied and improves the performance.
On the other hand, this makes it more difficult to write bash functions that call herbstclient. You can work around this by calling command herbstclient in your functions to still get some of the benefits of enabling this alias.