Hi Oleg,
1.) Local trains in Japan don't have seat reservations because they are usually used for travel on short distances and it would be a pain to reserve a ticket every time you needed to take a train ride for 10min. Other train types such as limited express trains and the Shinkansen do have seat reservations. This because they are generally used for longer distances and it is nice to know that you can sit beforehand.
2.) You can take a non reserved seat if all reserved seats are taking. You can always stand in the rare occasion that all seats are taking, so you don't have to worry about not being able to hop in your train.
3.) Seat reservations cost 200-700 yen depending on the train and route that you are traveling on. Making seat reservations is free if you have a JR Pass.
4.) Seats can be reserved from 1 month in advance up to 5 minutes before departs. Generally trains do not sell out but it is very much recommended to make seat reservation 2-3 days ahead of time when you travel on national Holidays such as new year or golden week.
I hope this helps!
Daniel