After some research I create an own solution.

For non-ajax part you need to disable input in form submit event when submit is not prevented by form-validation.

// $root is scope where to find input submits
notAjaxInit($root: JQuery): void {
        $root.find('input[type="submit"]:not(.ajax)')
            .each((i, input) => {
                const $input = $(input);
                const form = <HTMLFormElement>$input.closest('form').get(0);
                // on form submit
                form?.addEventListener('submit', e => {
                    // check if validation does not prevent submittion
                    if (e.defaultPrevented === false) {
                        // disable by class, not by property (corrupt form data)
                        input.classList.add('disabled');
                    }
                })
            })

    }

For ajax forms, which are handled by Naja you can achieve this by extension.

naja.addEventListener('before', event=> {
            if (event.currentTarget) {
                const $el = $(event.currentTarget);
                if ($el.is('input[type="submit"]')) {
                    $el.prop('disabled', 1);
                }
            }
        });

        naja.addEventListener('complete', event => {
            if (event.currentTarget) {
                const $el = $(event.currentTarget);
                if ($el.is('input[type="submit"]')) {
                    $el.prop('disabled');
                }
            }
        })

Bonus tip: you can init non-ajax part also with naja like this:

// document ready
naja.addEventListener('init', () => this.notAjaxInit($('body')));
// snippet update
naja.snippetHandler.addEventListener('afterUpdate', (e) => this.notAjaxInit($(<HTMLElement>e.detail.snippet)));