The reason for Kaisoku (快速) on JR not having surcharge goes back to Kokutetsu (日本国有鉄道) era. As explained on previous post, during Kokutetsu era there was a law called Kokutetsu Law (日本国有鉄道法). The law stated only three different trains in former Kokutetsu train service: Futsuu (普通), Kyukou (急行), and Tokkyuu (特急). Local trains (普通) fare requirement was base fare only (乗車券). Express (急行) and Limited Express (特急) require surcharge, Kuyykou-ryoukinn (急行料金) and Tokyuu-Ryoukinn (特急料金).
Kokutetsu Law even defined Unchinn (運賃) and Ryoukinn (料金). Unchinn (運賃) is a base fare, Jyousha-ken (乗車券). Ryoukinn (料金) is surcharge such as Tokyuu-ryoiukinn (特急券), Green car (グリーン券), sleeper surcharge (寝台券), etc.
Anyway, when Kokutetsu (predecessor of JR) introduced “rapid service” it was called Junkyu (準急) which was derived from Jun-kyukou (準急行) meaning “sub-express.” Kokutetsu Law only had Express and Limited Express for surcharge system. Hence Junkyuu (準急) was treated as local train without surcharge under Kokutetsu Law.
For long time rapid service on Kokutetsu was called Junkyu (準急) and terminology Kaisoku (快速) was seen only in private train lines (私鉄). First time Kokutetsu used the terminology Kaisoku (快速) was in Kansai area when new service called Shin-Kaisoku (新快速) was introduces in Nishi-Akashi – Kobe – Osaka – Kyoto. Now Shin-Kaisoku (新快速) service run far west as Himeji and far east as Tsuruga, but the original service was between Nishi-Akashi and Kyoto.
Today JR has many Resort Trains which run as Kaisoku with reserve seats. Because those train is Kaisoku there is no surcharge such as Kyukou-ken (急行券). However, there is surcharge for reserve seat (指定席券). Back in Kokutetsu days, Kokutetsu Law did not allow such surcharge for reserve seats because Kaisoku was classified as local train under Kokutetsu Law. Back in Kokutetsu era Junkyu (準急) trains did not have reserve seats.
Train geek.