Install manual hubs on 4WD, impact on value and handling?

On the other hand, the crafty upsell is

You can use 2wd low by engaging low on the transfer and not locking the hubs, which is useful for maneuvering a trailer.

So it is obviously worth more!

I have a trailer!

Adding 2wd low is a 20 minute modification on a Jimny with vacuum hubs, and then can be selected with a switch inside the car, so it's not particularly an advantage for manual hubs. If it's something you want then you can easily do it with whatever system you have.
I have manually selectable vacuum hubs in my Jimny using just 2 wires and a rocker switch, no cutting of the loom. Best of both worlds!

Coming from somebody who only 7 days ago bought his first Jimny manual hubs would have been negative for me, TBH I'm mature in age (not in mind), but I don't want to get out of the car & engage the hubs when I need them as likely or not it's going to be muddy & I don't want to get muddy   I would expected to pay less for manual hubs even though they would have cost the owner more, but I think it's a personal choice.

However if it's a warranty claim then it should go back to the cars original specification not what the dealer wants to give you.

I wouldn't get too hung up with getting out of the car to engage 4x4. It's very unlikely that you will ever be in a situation where you need 4x4 without some prior warning. If I am going off for a day on the lanes or the forecast is for snow then I lock the hubs in before I set off and leave them in, I then just use the buttons to get 4x4 as I need. Same goes if I'm intending to be towing out of fields. What I'm saying is you don't need to do the hubs each time you go in and out of 4x4.

I don't want to get out of the car to engage 4x4, it's snowing or axle deep in mud when I need it, why would I want to get out ?
I also have an RAC relay card and a mobile phone should it ever breakdown, don't see the need to carry spares.
it's a very personal thing this manual hub thing