It can be difficult to accurately estimate known quantities of coding work, let alone all the random unforeseeable adjustments that likely arise while working on a VN like this. This isn't a "slap on a few sentences and ship it" game, I believe the author spends time on the writing and probably adjusts/scraps things as better approaches are found. That usually comes with timeline-delaying stuff like coding tweaks, the need to create new art or adjust old art, reluctance to leave threads on the cutting room floor and cut off a storyline too soon, etc.
We're not in AAA deadline land, so we lose regular scheduling but get products that better reflect what the creator wants. I think that's a good thing even though it sucks to wait (because the game and story is so good). Some weeks, it feels like my project teams at work spend more time quibbling over price estimates/timelines for higher-ups than focusing on getting valuable work done for clients. It can pay to be patient, letting the experts focus on what they do best, resulting in a better end product. Just food for thought.