Indeed, as i said, "unless it's strongly connected to the story". But in general i take it as a symptom at misleaded design. As i often point, VNs are in the "choose your own adventure" category of games. Therefore they are supposed to let you choose your own adventure as much as the platform allows (which, yes, it's not much to begin with but still a dev should make the most of it). Since those are erotic/porn/dating simulator games, "your own adventure" orbits around to which LI you will pursuit. So, in general, "you WILL pursuit this LI and maybe some other" is not a good approach. IMHO.
You're right, a good portion of VNs are in this category - they tend to be the more 'sandboxy' ones, though.
The others are more oriented towards the novel-part and not as open.
Even in text format, it is time-consuming to write all those alternate content paths. In VNs, this means you also have to script and most important build the scenes for and do the renders for those paths. And in case you want to tell a specific story, that is a lot of resources used for something that isn't your focus.
Regardless of what choices you implement - there will always be those, that would like to have another choice in there.
Also, unless they tell us, only the devs know what will happen in the future, and if something we don't see a reason in has to be like that or not to make sense.
I'd advocate to trust in a dev to make good decisions for the story they want to tell.
In the end, I just don't think the 'open sandbox' style is better than others per se or the holy grail of VN development.