The contractors are correct; some time ago furnace manufacturers stopped making horizontal type furnaces and use regular type (sometimes they require simple conversion) for horizontal installations.
The regular 80% AFUE efficiency furnaces require traditional chimney for venting, high efficiency furnaces which have 90% + AFUE efficiency (depends on their manufacturer) use PVC vent pipes for ventilation which can go through the side wall or through the roof.
The chimney can be used only as a chase for those PVC vent pipes and only if there’s nothing else venting into it anymore (a water heater, gas fireplace, etc). Also, for the PVC pipe to be installed inside the chimney it would have to be straight / not a corbelled (angled) type chimney.
Regular type gas furnaces cannot be vented into an unlined chimney, so if you are replacing your furnace with 80% efficiency appliance, the chimney must be updated to the current standards (lined). As for the PVC vent pipe terminating above the deck, I don’t know if this is the only possible location.
There are several restrictions guarding vent pipe installations (so maybe the above your deck is the only available spot) and there will be condensation developing at the exhaust end of the pipe which will most likely cause deck discoloration because it is slightly acidic.
However, the vent pipe should be sloped towards the furnace so the most of the condensation will be discharged at the furnace’s end; there must be a floor drain / sump pump nearby, or a small pump installed to remove condensate from the appliance.
One more thing about the chimney
; if you have a water heater venting
into it as well and you decide to go with a high efficiency furnace, the chimney might become too large (in diameter) to serve this single appliance only and still require new liner (WH cannot be vented into an unlined chimney anyway).
I don’t know the layout of your house so I can’t really suggest much, let me know if my explanation triggered additional questions, just click “comment” below.