Thanks for clarifying this @Radek! And for your patience here 🙂
WordPress’ filtering of text values for security purposes unfortunately limits the easy with which spaces can be used here, so I had to write some custom code for you to enable this. I will explain how to go about getting this to work on your site – I hope it helps! Here goes:
Admin cost field
In the admin-facing cost field for events, just leave your prices without spaces in them. So, to use your example of 12 599 Kč, you would enter this in your edit-event screen as 12599. Here’s a screenshot of this:

Custom code
Now, to get that to display properly on the front-end, add this bit of code that I wrote for you to your theme’s functions.php file:
add_filter( 'tribe_get_cost', 'tribe_support_1016785', 10, 2 );
function tribe_support_1016785( $cost, $post_id ) {
$czech_format = number_format( absint( $cost ), 0, '.', ' ' );
return tribe_format_currency( $czech_format, $post_id );
}
How it looks
Once I added this custom code, here’s how things looked on the front-end of my site:

I hope you find similar success and that this helps!
Cheers,
George