I haven't measured latency, but there's nothing noticeable in my day to day experience, which includes gaming as well.
The desktop only goes through the KVM and the MST hub. The laptop additionally goes through a dock. I don't consider the devices to have the same purpose at all.
The dock serves several purposes for me:
1. Single cable to manage when taking or bringing the laptop (just one Thunderbolt carries all signals and power).
2. USB hub, as my laptop only has two USB ports.
3. Wired ethernet for the laptop.
4. Cable management - everything else plugging into the dock (audio, DP, ethernet, several other peripherals I use for day job).
The KVM is a switch and serves a different, specific purpose:
5. As it says in the name, switch inputs and outputs across multiple machines.
And the MST hub serves yet another purpose.
6. Allow one DP out to carry signal for multiple monitors.
There are KVMs that can act as an MST hub, but I wouldn't expect any latency difference there. It's still performing the action of presenting two displays to a single DP output. There are also monitors that support MST. Those monitors were much more expensive than mine when I was purchasing. The MST hub was a cheaper option for me than either getting a new monitor or getting a KVM that included such functionality.
Whether MST goes through an embedded hub in a KVM, or through an external hub, or through an embedded hub in a monitor, I'm not sure I see where any configuration would win on latency. They all need to do the same thing.
The thunderbolt dock also serves a different purpose than the KVM.
My laptop has decent connectivity - onboard ethernet, 2xUSB-A, 1xUSB-C/Thunderbolt, power. I would need a USB hub. So I could definitely plug in all of the cables every time I bring my laptop to my desk. I prefer not to. The Thunderbolt dock allows me to tuck away all of those extra cables and just run one to my laptop. Additionally it lets me keep the charging brick packed in my laptop bag. If I didn't have a dock, I'd have bought another charging brick.
My desktop has more connectivity than I can use, but it doesn't have Thunderbolt. It doesn't need thunderbolt. And I don't want to spend money or space for a PCIe Thunderbolt card that I do not need. And I didn't have any need for Thunderbolt or a KVM when I built my desktop.
There may be a thunderbolt KVM, but I didn't come across them. But I'd need to buy other hardware for my desktop. Or I'd have to find a KVM that can switch between a thunderbolt input and a DisplayPort/USB/Audio input. Such a device, if it exists would likely be quite expensive.
I don't know of any KVMs that also provide ethernet, nor do I want to switch ethernet among my computers in the manner that a KVM switches. So I'd still need to run multiple cables to my laptop whenever it comes to the desk.
So, our setups may be different, but I need all of the functionality I described above. I haven't found any single box that will do it all. I am perfectly happy to build a solution as I've described out of multiple components. And I will continue to get value out of each component, even as my setup changes.
The MST hub is great, because I can run one cable to the back of my monitor from any DP device and have a two-monitor setup. This is sticking around regardless of the rest.
The KVM will have use as long as I have multiple computers.
The dock will be valuable as long as I have a laptop with a thunderbolt port.
A hypothetical dual thunderbolt KVM with MST is more limited than the current setup. Its only potential benefit is some desk space, but even this can be managed just fine. The dock is on its way to mounting behind the desk.
As for system latency, my understanding is that the only additional latency from the KVM should be in USB peripherals, as it does serve as a USB hub. The audio and video signals are passed straight through so far as I know.