There are excellent answers here, and all I can do is contribute a fragment of one possible interpretation (that surely pales next to those already provided, and might be purely coincidental though I'm not conivinced):
By loose analogy the bees in Blade Runner 2049 may serve as a reference to the standard tune, "A Taste of Honey", which waxes about a love that "awoke [the singer's] heart" with a kiss, and that the singer "will return" one day. This mirrors Deckard's situation, and one of the notable recordings of this song was done by Billy Dee Williams, who played Harrison Ford's character's best friend (from his youth) from the Star Wars films.
As performed by Williams, the lyrics are:
A taste of honey
Tasting much sweeter than wine
I dream of your first kiss
And then I feel upon my lips again
A taste of honey
Tasting much sweeter than wine
I will return, yes I will return
I'll come back for the honey and you
Yours was the kiss that awoke my heart
There lingers still, though we're far apart
That taste of honey
Tasting much sweeter than wine
Oh I will return, yes I will return
I'll come back (He'll come back)
For the honey (For the honey)
And you
Further examination of the "bee" motif throughout literature and movies, and how it is interpreted in psychoanalytical contexts, may shed more light on this metaphor, although even concrete evidence as to why it was chosen for the film may never tell the "whole story" of a creative process.
A letter from C. G. Jung from 1934 to an "Elined Kotschnig" (found here in Volume I of the Letters of C. G. Jung) explores how the symbol of bees may have had a particular relevance in one person's dream, but some of the themes discussed therein may be broadly applicable. Being a historic document of some note, it is also not inconceivable that this letter itself may have had some direct or indirect influence on the film's use of the metaphor.