I came across some of thoses mangas that lies in the borderline of shonen ai and not.
some of them are stories in which main character is clearly not in a BL relationship, but side characters are.
would you consider manga with non-main theme shonen-ai as a shonen ai? or does it have to be a main theme in order for it to be considered shonen-ai?

some examples
The Tarot Cafe
Seimaden
Hana Kimi
Legend of Nereid

feel free to list other non-main character BL as you see fit

You make a good point. I would still consider the manga shonen-ai if it contains it. However, it's just a little part of it and many people like looking at the genre tags to get an idea of what the manga is about quickly. So it may give them the wrong impression that that's all the manga amounts to. Also people would use the genre search my have omited the manga because of the tag.
If you think about, it's like would you consider sex scenes and nudity in a manga hentai? It wouldn't if it's not all about that. So, I guess you should tag the manga according to what it mainly is.

On a side note, I would like to say I loved the shonen-ai in Hana Kimi, I especially the school doctor's story. It was touching and this was during the time when I didn't start reading shonen-ai yet. Actually, it may have been my first time. I don't really remember, I've read too many now.

Well, I wouldn't consider it shounen-ai unless it was a main part of the plot.
I would just say that it was a shoujo (or whatever type) manga with shounen-ai parts.

Well, I'd go by the extremity.
An adventure manga that has 50 pages
of explicit orgies, nakadashi and who knows
what would count as hentai to me, so
I'd consider stuff with intense man to man love
BL, even if it is not on every page.

Hm, technically, it is not.
The genre by which a manga (or any kind of media) is categorized is defined by the main theme.
Most mangas accumulate many different layers of content, since an adventure manga does not comprise of adventure alone but mostly has romantic aspects as well as a slice of life component (exemplary). Life has many facets and since art imitates life to gain realism, manga has more than just one theme.
We devide them into genres to distinguish them more easily from one another and sort them out according to our overall preferences and calling a science-fiction manga that focuses on the science-fiction a BL manga, just for the existence of BL, would actually contradict the system.
Hence, genres would be meaningless in the first place.

If it is a prominent theme, BL should be added as a subgenre.

Jeez, I just realized that if I put together what has been said before, my post is old news. Damn 😉