a few things:
first, the finished basement will appraise out higher then fiber cement siding. Also it will typically increase your taxes as well.
For the siding option, look around and see what other houses in your area are. If they are vinyl, stick with the vinyl.
You can also looking into using LP Smartside. I personally think it looks better then JH, and it runs around the same cost. Install is much easier so typically it falls right between JH and vinyl price-wise.

I think it depends on your area. I know that most of the homes in my area are hardi and that appraisers count it as masonry. I also like to custom paint. But if your area is mostly vinyl I would not pay the cost.

Not sure of maintenance.

I just spoke with our siding sub and he discussed Hardie and SmartSide siding options with me. He said that in Northern Minnesota they have switched to installing mostly LP SmartSide unless the customer asks for Hardie. I like the idea if cement board siding on my house over the wood fiber Smartside, but I'm worried about all the horror stories about moisture and chalking issues with Hardie. Anyone have experience with LP products? If I went with SmartSide, the installer would also use the LP trim for windows and other details. He said LP (vs. Hardie) has a much less expensive product for that cedar shake look in the gable ends as well.

you cant go wrong with the LP. Great product, good warranty. I think its one of the best looking composites as well. The LP still needs caulked however. About the only real true maintenance free option will be going with vinyl.
For your climate zone 6, I would be far more concerned about air sealing and moisture/drying/insulation levels within your wall and not what is covering it.

Our builder is using r21 in the walls and a full house wrap (Tyvek)

It is not too late to add insulation upgrades. I was thinking about doing spray foam, but my builder said it was not "worth it" from a cost perspective. What can I do to increase R value with a minimal cost? I was told that foam would end up costing about $10 - $12 thousand more than batts. Is that really worth it? I have never had a house with spray foam insulation before.

your builder is correct. Spray foams, even open cell, is usually not worth the cost. It creates a tighter air barrier, but only at the stud plane. It fails to address air leaks at the top and bottom sills, as well as around window opening framing. Spray foams, r value wise, perform slightly better then batts, but you still have thermal bridging issue. Untill you address that, anything you stuff between the studs will suffer a loss r value of 15-20% reduction. The best thing you can do is add exterior foam sheathing. XPS is r 5 per inch. Adding that greatly boosts the performance of what is inside the walls. However for your climate zone 6, to avoid dew point issues and condensation inside the walls, you would need to go thicker then 1".
The cheapest thing you can do to make the biggest difference would be to caulk/seal your walls as best you can. Go around and caulk the bottom plates to the subfloor, the sheathing to the studs, the cracks between the top plates, etc etc etc. The more easy air sealing you can do, the better. Air moving through the insualtion continues to reduce its performance, especially with batts as the weather gets colder. (your "r21" batt performs even lower when the temps decrease).
However the walls arent the only thing. THe ceiling also is a massive source of air leaking, especially with the use of many can lights that is popular today. Even the insulated "air tight" cans leak. Air sealing has to be done at the ceiling plane as well. THis is typically done from above after the drywall is on.
If you want a slightly upgrade, I would ask him about blown cellulose of fiberglass (such as Spyder). This will perform much better then batts as it will fill the entire stud space that batts never do. It would be an upgrade, but a blown/dense pack product mixed with air sealing will pay for itself in a very short time. Building new is the best time to add energy improvements. They start saving you money from day one. The same can not be said for upgraded siding, counters, cabinets, etc.

We are already getting r50 blown fiberglass in the ceiling. He also added "Thermax RIM" (I'm not sure what this is). The poured basement will get R11 batts in the walls.