You have 1000 uncompressed images on your first release. First. How big will you project your final file size be? How big a percentage of the overall story have you shown so far? If you're planning ten releases at an average of 1 GB a release, that's 10 GB for a visual novel. If you're planning 30? OMG...
And absolutely, padding hurts the player experience. Indirectly, the download will be a bitch considering it's a visual novel and not a game. Directly, constant quick cutting (because we're certainly not going to dwell on a second or third image of the same thing) hurts the eyes and tires the mind. Bad pacing, the inevitable consequence of putting too much in, is very annoying. It doesn't "feel like more of a scene" (especially since there is nothing here soothing the mind in the optical way 24 fps does), it feels like you're milking time. It feels like, well, padding. When you're watching a a car scene in a movie, you don't watch the entire 30 minute drive from point A to point B. That's boring and unnecessary to the experience of a story. You don't watch the driver fix her mirror, make her hand signals, fiddle with her Spotify, etc. Unless that action leads to something that will enhance the experience, you do not need it, and you delay the journey the audience is taking with you for absolutely nothing. You're like a museum guide who stops to comment on the texture of the velvet roping in-between painting exhibits.
And absolutely, yes, writing efficiency. It's not just for training manuals. And this is especially important because a. you're working with a team and b. eventually you'll be taking patron money for this. And judging by your response, you have no clue how enormous the amount of "pertinent details" are, especially in a collaborative creative work. Writing efficiency means that I am able to give every necessary writing detail on my end with as few revisions as possible (meaning that any revision will be due to compromises and additions due to collaboration and not because "I forgot to add something" etc), so that the other person can do her job as comprehensively and efficiently as possible. Have you seen a movie outline? A sequence treatment? A shooting script? Story board? Those are not "simplified". In fact, by the time the camera rolls, there should be as little room for mistakes as possible. I can't go to the director in the middle of viewing the day's rushes and telling him he must reshoot a scene to add this silly joke I came up with. If your visual teams is spending more time rendering unnecessary images, it's because you guys went ahead without enough of the "pertinent details". Hell, if that is indeed your "standing order", then much of the inefficiency and unnecessary padding is rooted on your end and not his.