As to your question 1, I would say it is quite safe to walk around the area at night since I have never heard anything bad about Ninennzaka and Sannenzaka.
It is a very quiet residential area, so please keep quiet when you walk around after 11pm. Also, lanterns are lit until 9:30pm.
As to your question 2, I would recommend you to enjoy sightseeing with a bicycle since the road gets congested and buses are always packed.
Please note Japan is a country where bicycles keep to the left side of the road. Also, you cannot park on the street or road, so please use a parking lot for bicycles.
Reference:
http://www.kyoto-option.com/english/
http://www.cyclekyoto.com/bike-rental
http://kanko.city.kyoto.lg.jp/bicycle/en/rental/
As to your question 3, basically it should be reliable, I think.
There are 2 more companies which provide the same kind of service.
Kyoto Station Chuo Exit:
http://carry-s.com/wp/?page_id=71
Hachijo Exit:
http://delivery-service.jp/travel_bag.html
According to the reputation, there are not much differences between those two companies, but when it is crowded, the service may not be as smooth as usual. You may want to ask the front desk at the hotel. They might have more information about it.
