How fast can through hole PCBs run?
The core of processors usually runs quite a bit faster than anything on the board. I would guess the fastest buses on that board are probably running on a 33 MHz clock.

In general the most important thing with high-frequency work is to keep return current loop area low. You do that by running the tracks closely above or below a reference plane, avoiding changes of reference plane as much as possible, avoiding cutting up your reference planes as much as possible and tying together your reference planes (either directly or with capacitors) as close as possible to where tracks change reference plane. 

Unfortunately to do that well really requires at least 6 layers. In mass production PCBs are dirt cheap, so a 6-layer board doesn't break the bank but for one-off work the costs get seriously painful. 

The trouble with through-hole ICs is that they end up with significant connection lengths inside the package which unless it is a fancy specially designed package have no reference plane, pushing up the loop area. The higher the pin count gets the worse this gets. 

Though-hole connectors don't suffer nearly as badly from this issue and have remained in widespread use to this day, even for very fast connectors. PCI-X puts a multipoint bus with a 133 MHz clock over through-hole connectors. PCIe runs at 8 gigatransitions per second (giving a "worst case fundamental frequency" of 4 GHz) over through-hole connectors.