I just picked up a 06 353 last month. Previous boat was a 99 baja 25 Outlaw. When I winterized that I always removed the batteries and stored them. The 353 has smartcraft system on it. My question is if I remove batteries for the winter will it cause any issues with the computers like a reset or something? Baja didn't have much in the way of new technology in it so I gotta learn some things

Highly unlikely. I assume you switch the batteries off when the boats not in use... so.. same thing?

1) It's best to store your sterndrive boat with the drive(s) in the down position, as it's better for the hydraulics, and doesn't stretch the bellows/boot around the input shaft.
2) The reason I DON'T like removing the batteries from the boat for winter storage, is that if you are storing the boat with the drive(s) installed and down, if you NEED to move the boat during storage...
...you have to go back and install the batteries to trim it up and move it.
If you have shorepower and/or an onboard charger, I just recommend keeping it plugged in. That's worked for me for my boats.

You should disconnect batteries, any parasitic draw on them will drain them over winter and if stored in NY (where it lists your location) you run the risk of them freezing. I don't believe it will have any affect on your smartcraft, but please post an update come spring

What do people do in colder climates to keep their batteries from freezing in their cars?

I have never heard of a battery freezing?

fully charged battery will not, unless it gets really cold (-80F -ish). However a discharged battery will.

Apparently I need more 10 or more posts to add a link, but google Frozen Battery. Sometimes they can be thawed and recharged, but sometimes ruins the battery.

Heated Garage fixes frozen battery syndrome. and it's double insurance against a cracked block (I also winterize).

Back when the garage was not heated, I would remove the batteries and store them in my basement on a good charger.

dead batts will freeze and possibly crack.