While the dancers were performing on the stage, the audiences were applauding heartily on the seats. -"on" the seats? Is "in" more suitable?

Yes. "in" is more suitable.
It is even more fluent by saying "in their seats"

"On the seat" 與　"in the seat"都有人用，但是涵義不太一樣．
＂ｉｎ．．．＂一般用在＂低而舒適＂的座位，像是沙發躺椅之類的．強調溫馨，舒適．
＂ｏｎ．．．＂一般用在＂座椅功能＂與＂指定位置／座席＂．強調功能與席次．

在你的問題原句（其實是爛英語）後者＂ｏｎ．．．＂是比較合適的．
因為音樂會的座位都是指定座席的．

例句們：

His house is so cool and you can play computer games, watch TV, and have dinner in your (my) seat (without moving your butts).

On your seat, please, kids, so that we can make sure everyone has a spot.

還有，我有說你的　問題原句是爛英語　嗎？
可以再說一遍嗎？

問題原句是爛英語！

至於＂ｉｎ＂＂ｏｎ＂＂ａｔ＂的使用場合，也只有大慨的規則．不管你信誰，都是例外一堆．其實你讀幾本好書以後，自己就會龜納出來．根本不必別人教．你要記住的是，不要吹毛求疵！體會作者想要表達的差別．３個月後就運用自如了．

While the dancers were performing on the stage, the audiences were applauding heartily on the seats. -"on" the seats? Is "in" more suitable?

While the dancers were performing on the stage, the audiences were applauding heartily on the seats.

正當舞蹈演員在舞台上表演的時候，在座位上的觀眾都報以熱烈的掌聲。

“on"表示在xx上面

“In" = 在xx 内𥚃或裡面

“at” = 於某個日期或地㸃

所以此例句的“on”the seats是必然的囉！

謹供参考, 謝謝！🤔

You can sit on a chair. = You can sit in a chair.
新世紀英漢辭典p.1291 sit
seat是所有的chair, bench, sofa等可坐之物的總稱

但英文有不重複的習慣,本句的前面用了on the stage, 則後面的介系詞片語宜用in the seats.

No!

If you are "in" the seat, you are inside the seat(cushion/wood/metal).
The function of preposition is to describe or relate something in a logical and rational way.

中文人對於"坐"會認為"坐在座椅中"是正統，所以才會感覺坐或座椅是"正中"才正確，「上坐」或「坐上」是特別的尊敬的意思，語句感覺上，坐在椅子"上"感覺並非"常態"，或者另一想像是"蹲在椅上"了，所以有不雅感。有些英語詞當你用"中文"想像的話是會跟它們不同的，要學好英文先要明白這些分別。

英語的"on"是真真實實的在某東西"上面"/"頂部"/"被托起來"。"in"就真真實實在某東西"裏面"(包括時間和空間)才會用in.

說一個例子：
講月份(Jan, Feb, Mar...Dec)的preposition必定是用"in"的，因為一個月裏有數十天，講/寫在某月"裏"是指那月的眾日子的當中(但沒有講明是那一天)，所以在某月(中)。
假如你寫出個日子(11月24日)是一個確定的日期，英文必定是寫/講on 24th of November或on November 24. 英語在某日子"上"便是中文在這日子"裏"。因為英語邏輯在講日子時已經是最細單位，你只能"站在"它的時空上面，就算講一些在當天裏發生的事也不會講在某天"裏"。