Hello again,
1.) Yes you can use the Suica card for travel on the shinkansen for using non reserved seats.
I would however recommend buying a train ticket at a ticket counter, this way you can arrange for seating together. Which I would certainly do, traveling with a family.
2.) This depends on the amount of travel you do within a day. With Suica you pay the normal ticket fees but it does not limited you to one kind of transportation. The one day metro pass is a great deal but it is only valid on the metro, I would recommend buying it if you plan to do a lot of sightseeing in Tokyo on a single day.
3.) You can charge the Suica card by amounts of a 1000 yen or multiples thereof, the maximum a normal suica card can hold is 20,000 Yen. You can always return a Suica card to get a refund for the deposit and renaming balance.
A fee of 210 Yen applies if you still have balance on the card.
4.) I looked for buses but unfortunately could find none departing around midnight (the last I could find leaves around 8 p.m.). Arriving around midnight will make for difficulties. Public transport shuts down a little after midnight and the only way to travel around will be by using a rather expansive taxi. Consider booking your first nights accommodation around the Airport or around Tokyo station, the Mono rail is available until 00:10 you can use that to travel to Yurakucho and use the Yamanote line from there to travel to central Tokyo. You can read more about late arrivals at Haneda Airport here.
Hope this helps,
Daniel