For Nagashima Countdown, Mie Kotsu, Sanco Bus, runs at least 4 special buses to Kuwana station.
Sanco Bus from Nagashima Onsen to Kuwana on 1 Jan.
1: 00 30
2: 00 30http://www.nagashima-onsen.co.jp/cdnyparty/access.html/http://www.sanco.co.jp/foreign/english/index.html
Meitetsu Bus runs 16 special direct buses to Nagoya over the night.http://www.meitetsu-bus.co.jp/info/detail/525
Kintetsu Railways runs over the night. Here are some timetables.
Kintetsu Nagoya station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/17048...
Kuwana station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/17036...
Kyoto station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/50051...
Kintetsu Nara station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/30231...
Osaka-Namba station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/10051...
Toba station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/19009...
Ise-shi station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/18017...
Ise-Nakagawa station http://www.kintetsu.co.jp/railway/Dia/newyear2018/kakueki/171231/20521...
So, there should be no problem. Nagashima Countdown is just a western favor event, primarily for the youth generation. On New Year's Eve, Omisoka in Japanese, the Japanese eat Toshikoshi Soba (noddles over the year), hear Joya no Kane ring (bells of temples ring over the year), visit a shrine for Ninen-Mairi (over the year visit) or Hatsu-Moude (the first visit of the year), and see Hatsu-Hinode (the first sunrise of the year). A significant fraction of Japanese does not sleep from Omisoka to Gantan (the morning of New Year's Day). They get up late on New Year's Day, Ganjitsu, eat Zoni (Mochi, rice cakes, in a soup), and go to Hatsu-Uri (the first selling) on this day or later.
Nara and Kyoto are full of temples and shrines. There is the top shrine Ise Jingu in Shima Peninsula. This peninsula is a good place to see Hatsu-Hinode. That is a reason for the overnight operation of Kintetsu Railways. Along with Kintetsu, Nagoya Subways, Osaka Subways, and others also operate over the night. Here is a map for JR West for your Kansai-Hiroshima Pass. The east edges are Kusatsu and Sakurai stations.https://www.westjr.co.jp/press/article/2017/11/page_11531.htmlhttp://www.isejingu.or.jp/en/index.html
Here are some statistics for visitors.
Atsuta Jingu Shrine (Nagoya): 2.3 million visitors during 1-3 Jan, Sanganichi
Ise Jungu Shirine: 500,000 visitors during Sanganichi
Futami Okitama Shirine, Meoto-Iwa (Shima, sunrise at around 7:15): 70,000 visiters on Jan 1
Fushimi Inari Shrine (Kyoto): 2.7 million visitors during Sanganichi
Yasaka Shrine (Kyoto): 1 million visitors during Sanganichi
Kashihara Jingu Shrine (Nara): 1 million visitors during Sanganichi
Sumiyoshi Taisha Shrine (Osaka): 2.5 million visitors during Sanganichi
Ikuta Shrine (Kobe): 1.5 million visitors during Sanganichi
Minatogawa Shirine (Kobe): 1.1 million visitors during Sanganichi
Nagata Shirine: 700,000 visitors during Sanganichihttps://travel.rakuten.co.jp/mytrip/ranking/newyear-hatsumoude/http://winter.walkerplus.com/detail/ar0624s31432/https://www.travel.co.jp/guide/matome/1/https://innocence-life.com/kansaihatsumoude-matome/https://innocence-life.com/tokaihatsumoude-matome/
So you could select any set of such events, such as
Dec 31: Nabana no Sato and Nagashima Countdown, Hatsu-Moude in Ise, Hatsu-Hinode at Shima Peninsula
Jan 1: Sumiyoshi Taisha and Hatsu-Uri in Osaka
Dec 31: Joya no Kane, Ninen-Mairi or Hatsu-Moude in Nara or Kyoto
Jan 1: Nabana no Sato
In the case of Dec 31: Nabana no Sato and Nagashima Countdown only, this would be the fastest route to Osaka: Nagashima Onsen 100-(Sanco Bus: 10 min)-110: Kuwana 117-(Ise-Shima Liner: 40 min)-200: Ise-Nakagawa 207-(Urban Liner: 80 min)-330: Osaka-Namba. You would see many Japanese who wear Kimono or Furisode on the way to Ise.