We are using the Standard Sales Order PDF/HTML template... but we have an error: item.quantity is printed with "," as decimal and "." as thousands separator... while item.rate and item.amount are using the oposite: "." as decimal and "," as thousands separator... Where can I change item.quantity separators?

There are two different settings that are at play, and probably why you have different formatting: For all non-Currency fields (Decimal and Integer) the Number Format under the company General Preferences will be used. But, for Currency field, the currency can have Override Currency Format checked, and if it is, then a currency=specific formatting can be applied that may be different from your company Number Format. Try checking these settings to see what they are currently set to.

Thanks for the hint @scottvonduhn