You can use e/OS (pretty good de-Googled Android OS) and overall stop using Google services (look at Europe, they are also in the process of showing the middle finger to big tech). NewPipe itself said you can load the app via ADB onto your device (this can be daunting if you are not technical but tutorials will help you).
Overall I can just recommend to see this as a point where you switch away from big tech, that collects data and pushes you into their way of living. There are FOSS alternatives for almost all Google, Microsoft and other "You will need this to function in our civilization" bull shit services. I study, live and work completely FOSS since 6 years (exemptions are of course present, like government applications or e-banking), and I never had any problems doing my tasks, finding a place or having fun with friends.
Break yourself free, believe me, it is healing.
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.