Probably quite a bit - a port isn't just a hole in the case big enough to take the connector, you know - the connectors are bigger on the inside and need to be mechanically supported. Ports need controller chips and misc. other resistors, capacitors etc. Also, the computer needs enough power supply capacity to cope if every Thunderbolt port demands its regulation 10 W of power.
On one side of the rMBP the logic board runs alongside the edge of the case to support the TB and USB ports - on the other side there's a large-ish i/o board to support the ports on that side. Less ports mean more flexibility on positioning the logic board - so on the new MacBook it seems to be at the centre rear of the machine, where the case is thickest .
You do know that Intel are switching to
new, thinner connectors for Thunderbolt 3?
They wouldn't be pro devices without Ethernet, ExpressCard, Firewire, optical drives, SCSI, ADB, NuBus, floppy drives, LocalTalk, RS232, Centronics, IEE488, Kansas City, 20mA current loop, S-100...
Reality check: "Pro" is a marketing term meaning "more expensive than the version that
doesn't have 'Pro' written on it.