This exact thing has actually been a benefit to physical media, for me at least. 
I try to split my reading time between doing something physical and something on the computer. So when I’m reading on the computer, I get access to stuff like yomichan, jisho, textractor, or even deepl to quickly try to answer questions and look up words.
But, when I’m reading physical stuff I am really restricted to only looking up stuff that I absolutely need to look up to understand things. Forces me to try to turn the brain gears a little harder, and also to tolerate more ambiguity than I’d be comfortable with accepting when reading something digitally.
I know it’s really hard, but try not to worry too much about the nebulous concept of “efficiency”
whatever you are doing that works for you is probably good. If you feel like it’s not working and want to try out other things, don’t get too hung up on making yourself do something you don’t enjoy just because someone else said it was efficient/stop doing something you do enjoy because someone said it’s inefficient.
In the long run, as long as you are doing reading and interacting with the language at all, you will make progress! You will build up your grammatical pattern recognition, you will start to recognize common words/phrases, you will start to get a feel for the flow of writing in japanese, and all that other stuff! The minutia of day to day study routines are more of a personal taste thing; what works for others might not be what works for you, and what works best for you might also change over time!
As for changing my strategy, I try to shake things up pretty often. I used to do a TON of anki and wanikani, but last september I swore of SRS when I first committed to reading a ton. The only form of note-taking I did was opening a new dictionary tab every time I looked up a word, and then copying them into a list, but I pretty much never looked at them again. I mainly used it as a way to track how hard a text was based on how many words I had to look up.
But just this last month, I started re-introducing anki (after I learned yomichan could automatically make flashcards lmao) just to see if I’d like it more now, and I have been enjoying it again and seeing benefits, so I might keep with it until I get frustrated with it again
It’s really a self-reflective thing, though. I try to pay attention to what parts of the reading feel hard, and then implement stuff to target those weaknesses so that my main reading can be as enjoyable as possible. When I quit wk, it was to focus on increasing my reading speed/endurance because that felt like my weakest skill. Now, my grammar feels pretty weak, so i’ve been doing a little bit of study for that on the side. But all the studying I do is another thing. I try to read mostly for fun; if I am really really struggling to read something (or just not enjoying it), I usually shelve it to come back to later and find something new.