I am actually quite happy, that NewPipe dose not show Shorts this way. I hate the modern YouTube, that when you search for something you just get bombarded with Shorts, instead of what you are looking for. Yes, there is a filter to sort them out, but this filter resets every time you change the search query.
I can understand that you want to have shorts without ads, everything is better without ads, but I hope NewPipe never adopts this.
Maybe you can use Brave-Browser and login there together with its ad-blocker.