Thank you for your early announcement to wake this part of the game from its long-time slumber, Piotr!
But I fear for quite grave balancing problems.
Interactions with and befriending of NPCs in bars are very nice and satisfying and meaningful at the beginning of the game, but just after a while it turns out as a more atmospheric goodie than a great (and scaling!) way of making money, xp and progress itself.
Almost only NPCs who can mod your submarine equipment remain relatively attractive; and even then it's only temporarily worthwhile to buff a friendship, because you don't "need" certain NPCs later "anymore" (well, related to NPCs and not people in rl, of course

).
Let's take Birgit in Hamburg as an example. She works at the shipyard in Hamburg and can buff your equipment for your Seahorse.
Once you go ahead and have aquired a Starfish, you never look back anymore for anyone who enhances stuff for Seahorses.
Moreover till you don't plan to advance to the almighty Barracuda, you won't be specifically interested in the Barracuda-NPC in Old York, neither (and even less given the fact that this once and/or "prematurely" built friendship would either decay over time or need constant nurturing and therefor a kind of uphold cost).
I totally understand the concept and meaning of decaying friendships - and would like to like it.
But if you implement these on top of an already very "fragile" added value for players to build up and invest into good and best relations to NPCs, then they will get obsolete for even interested players or even perfectionists like me.
Although with regret I would pump only relations to shipyard NPCs who benefit my current or next submarine class, and even then I would do this "just in time" to escape any later "decaying malus" (apart from letting the friendship decline afterwards to avoid said uphold costs, anyway).
And as it is already a kind of herculean and idle task to befriend all NPCs in the game - if you should be up to it as an atmosphere liking player like me -, the "decaying game" kills any meaning to pursue such an only enclosed aspect of the game, especially spoken in terms of wordwidely built up friendships.
Furthermore satisfying and immersive feelings, like returning to an old acquainted city full of hard-earned old friends after years of absence because of having sailed other corners of the whole seven seas for a long time, would die on top.
All friends and chummers of the past are back to neutral and pretend to be unknown to me just like at the start of the game? What a bummer!
And although there are only a handful of LPs for Aquabyss around on YouTube, even these few show drastically, that players neglect relation building of NPCs more and more after they were quite interested in this aspect of the game initially, anyway.
And that counts already for the status quo - and not for any future "decaying bummer" on top.
So it's hard to give a constructive advice on this matter, but here are my two verns:
Don't wake the "decaying factor" from its coded slumber as it would bereft a nice side aspect of this game of its last and lasting meaningful surplus.
Moreover: I can't imagine any constructive implementation of this debuff as it just hits and punishes only players who interact deeplier with NPCs - while careless players even profit from this "decay" in a competitive way as they haven't "dumbed" so many efforts, real and ingame time and quite some verns into now "decayed friendships over time".
But implement the friend/foe system; maybe a little defused, so it would take twice or thrice the effort to bond with both NPCs (or whole networks of them) who disdain each other at the same time?
Thank you for your hard and enduring work on this precious little gem of a game!
p.s.
To further strenghten the aspect of relations to NPCs: you could expand the list of "alltime best players" with a decidedly point system.
The number of made friendships in the game could count for this point system just as quite some other more symbolic aspects of the game, too (such as e.g. visited and known cities or the number of fulfilled contracts or even so far undocumented fulfilled personal quests).
So the sum of all accumulated points but not the highest player level (which would, of course, result in more points, too) would define the ranking and encourage players to pursue much more goals in the game than until now.