The main means of thermal dissipation are convection and radiation (and flow). Convection is used always and independent of orientation. Board setup of the era have been made in any direction.
Putting boards close and in parallel is, independent of orientation, not a great idea at first, as they heat each other (by radiation). This means for thermal dissipation the whole stack has to be treated as one, independent of orientation or packaging. Similar any closed case will only allow to equalisation within by means of convection/radiation/flow.
This only changes if there's an additional air flow across the stack/between the boards. This can for example be encouraged by an orientation that lets air freely come in from one side and leave (again freely) on the other side. I assume that's what the question is about.
To start with, typical S100 cases, like the Altair, do not really support airflow as the base board is in the way. In addition, there is usually a closed metal sheet direct above the boards.and often solid walls on either side.
In general thermal design wasn't a big issue for early machines as they combined low power consumption (in absolute terms) with huge volume, wo thermal density was quite low. Even loaded S100 machines did usually produce more heat in the power supply than along the boards (*1).
Of course situation was different in minis and mainframes, but they were as well designed for airflow. Here Mounting was usually on a backplane leaving room for a straight airflow across the boards - which usually was enforced by ventilators.
The Apple II did rely only on convection thru the plastic covers, as there was no real airflow design, despite the slots on the side and openings on the back. While this was fine for the low heat production of the basic machine even including a few cards, it only became a problem when really stacked, clogged with cables and operated in an hot environment (like with a CRT stacked on top blocking heat flow or even adding). Here solutions like Kensington System Saver added airflow. In relation to the question it's notable that the System Saver did simply suck out air on one side, square to the card orientation. This worked fine, as the effect of exchanging the air outclasses everything that relies on convection.
Still, it wasn't as much of a problem as Kensignton adds may suggest, as the as the original Apple II PS was rated at 38 Watt (*2). Still keeping over all heat production rather low. Of course, as soon as there was a hard disk to be build in, air flow became a must - in addition to a bigger PS anyway :))
The IBM PC in turn was already designed with that experience in mind. Here the power supply's ventilator sucks air out of the case - replenished via inlets on the opposite side as the PS was located in the back to the right and inlets were in the front to the left - in fact, right were (full length) expansion board would end up.
Still it's important to keep in mind that the IBM-PC was extreme low power from today's POV. The original PSU was rated at 63 Watt. Nop, no zero missing or so, it was that low. Combined with a case that large as the original PC, the design was more than sufficient to keep everything within limits.
Modern PCs with a much higher over all power dissipation have an improved airflow design with the power supplies ventilator forcing air out of the case, thus sucking in cold (room temperature) air via designated ventilating openings or simply any other opening (*3,*4). While focusing on CPU and chipset, this is more than sufficient to get all heat, including additional bards out, despite of board orientation.
The issue with added ventilators to certain chips/boards isn't the over all heat production, but local distribution (*5).
Long story short: Early systems didn't ned much air flow design and board orientation was more due case construction and handling than heat management.
*1 - Yes, that includes the (comparably) inefficient regulators on each board.
*2 - There is a real nice (as usual) analysis of the Apple II PSU as well the IBM-PC's by Ken Shirriff.
*3 - Who doesn't remember some PC clogging up floppy drives with lint as their case was missing dedicated air inlets.
*4 - Related were home build machines were users added ventilators pressing fresh air into the case, which of course increased inside pressure and exhaust true every possible opening, again including floppy drives, depositing even more dirt there.
*5 - Given,there are some high end cards that do have their complete own air flow, sucking in fresh air thru a desicated slot cover.