Both have about the same performance and unless the batteries are old, most casual users wont notice the charge length from a 48v to a 36v.
That being said there are things to consider:
48v batteries are 8v a piece with 6 batteries used, this is a perfect configuration other then you will pay more for 8v batteries as they are a specialized item. 36v carts use 6v batteries which are more widely availible and less expensive. Properly maintained batteries should last 5-7 years, though I see many carts come to us for repairs that have not been and 800-1000 for new batteries is never a good thing.
48v carts need a power converter to power 12v items. While you could run some lights at 16v, they will have a shorter life, if you want to power certain other accesories or add a charge plug for electronic devices, you will need a converter, they run 50-150 dollars depending on the unit. 36v carts do no need this, you can tie 2 6v batteries together and get a solid 12v power source and unless you are running a radio or other potential high draw items off the battery it will not unequalize the charge. EZGO ships their 36v street legal 4 and 6 seaters wired this way. The 48v carts chargers cost more if you have to replace or rebuild them.
If the used/rebuilt one has more of the accessories you want for the same price I would go that route. A rear seat kit is 3-500 just for the kit plus your time or someones labor to install. Light kits are around 100 bucks depending on the model, so consider those costs as well.
I would say as long as the older model year cart is low rust, the battery tray is in good condition and the batteries are less then 2 years old it is probably worth it if it has more of the accessories you want.