TL;DR: This is a habit and as such, him noticing you pulling away is unavoidable. The quickest and easiest way to break a habit is deprive him of his reward for a period of time. I'd suggest being straightforward and taking a two week break from the lunches and then approaching him about cutting down the days.
Why keeping it "inconspicuous" is hard
It's funny that you call this a "habit," because that's exactly what him inviting you and then eating lunch with you every day has become.
According to NPR, a habit is formed from 3 parts, called a "habit loop":
First, there's a cue, or trigger, that tells your brain to go into automatic mode and let a behavior unfold.
This is lunchtime at your work or his stomach growling or a glance at the clock right around noon.
Then there's the routine, which is the behavior itself
This is his invitation or him going over to your desk or however you begin your lunch.
The third step...is the reward: something that your brain likes that helps it remember the "habit loop" in the future.
This is you eating lunch together, namely his opportunity to socialize (which from what you said is rare) while also getting a break from work. If he likes you it's probably also getting spend time with you.
Because this is a habit and probably near automatic for him at this point, a sudden absence of your lunchtimes will immediately standout to him. He will notice that you're distancing yourself, no matter how you do it. As such, I'd like to challenge the premise of your question. I don't think it's possible to be "inconspicuous" here. That being said, what's the best way to distance yourself without ruining the friendship and making things awkward?
Breaking the habit
The NPR article goes on to talk about how to break a habit. Namely by removing the cue and reward. In your case, it's not possible to remove the cue, but you can remove the reward. I would suggest that you spend a week or two without having lunch with him. After that long breaking his habit, when you go back to lunch with him again it will be far easier to cut it down to a day or two a week without him pushing for more. He may also find other people to have lunch with in that time! No matter what happens, two weeks without you will help break his reliance on you.
A "conspicuous" solution
To do this, I'd be straightforward and tell him in advance that you don't want to eat with him for the next two weeks:
Hey [friend], I feel like we've been eating lunch together a lot lately and I've been wanting to mix things up for a while. I have some coworkers that I've been meaning to catchup with and things have been getting crazier around the office so I won't even be able to leave some days*--how about we take a break from all the lunches for the next two weeks?
*Feel free to swap this whole sentence up to the star out for any other personal reasons. You've just mentioned in a comment that you want time for personal reflection--that would be something perfect to bring up here! Or that you want time away from all of work--coworkers included.
Note that I've given three seperate reasons for taking a break in that excerpt (all of them true from what you said in this comment) and none of them insinuating that your coworker is at fault for this situation. You want to try to make this about you (especially if they're shy/self-concious!).
Once the two weeks are up, tell him that you'll be willing to do lunch 2-3 times a week, but you've found that you enjoy a little time to yourself to take a break from everything work related. At this point, as explained, he should be far more amenable to not eating every day.
Best of luck!