I agree with the importance of mastering reading and not memorizing every piece.
That said, you asked about deep learning and said that you currently just rely on muscle memory. Is that really true, or do you also remember the sound of the music and are able to hear it in your mind's ear, at least the melody line, perhaps even some qualities of the harmonies or the rhythm of the base?
As Dr Molly Gebrian and others mention, we will remember things better if we consciously manipulate the info somehow. Just to mention one approach: I find it useful to not just read a note but also hear and name it in the context of the scale using a movable Do scale. So, if there is an E in the key of F major I know that it's a Ti. After that short "analysis" I usually can not ever again unhear the "Ti quality" of the tone even if I originally was not paying attention to it.
For me personally, this functional approach works better than listening for intervals between consecutive notes. Though I can hear that the interval from a Fa up to the Do and from a Re up to La are both perfect fifths, my brain processes them very differently in a musical context and I much prefer the solfege/functional approach. Others may be wired differently.
Most people will need conscious ear training over an extended period of time to be able to hear with certainty what solfege scale degree a pitch is at (I certainly did!) so this is not a quick fix but a great tool once it's been mastered. I think it makes sense to spend just a couple of minutes a day to play something really easy by ear for practice. I didn't do this at first when I had lessons on recorder and clarinet as a child and I ended up over-dependent on sheet music. In retrospect, it would have been better if I had also developed some playing by ear from the beginning instead of having to catch up on that after several years. Most teachers who advocate for integrating playing by ear recommend very simple melodies to begin with, and also transposing them to different key signatures. Also, when learning a scale it helps to name the notes as you play them: do re mi fa sol la ti do ti la sol fa mi re do. (Or for minor scales: do re me ... )
Nowadays there are many ear training apps. For solfege I have used and can recommend Functional Ear Trainer which is available for both Android and iOS. The online tonedear has other useful exercises such as intervals, chords and chord progressions.
