Usually if you go to Magento backend you will find System- Scheduler - Job Configuration under Actions you can see "run Now" well in our Magento Store this option disappeared. I have no idea why, any advice?
That actually is a function of a module named AOE Scheduler. It has been removed in newer versions of the module for reasons mentioned on their github page.
Why is "run now" a bad idea and what should I use instead?
"Run now" should only be used in a cli context. That's why never versions Aoe_Scheduler disable the use of runNow from the web service API and the Magento admin by default. Instead of "run now" you should use "schedule now" which will result in a task to be scheduled and then being picked from the regular cron and processed in the correct cli context. Running a job in the context of the webserver is generally a bad idea since you could run into memory limit out timeout issues. Cron tasks are designed to run from cli and will usually run longer than 30 sec. Increasing your webservers memory limit and maximum execution time is also not a good idea.