We need to distinguish between "Arduino-like" and an actual Arduino. Actual Arduinos vary in quality (and therefore, probably, longevity) depending on who made them and how much, if any, consideration was given to the quality of the components used. There must be 50 companies out there making boards that carry the Arduino name so it's hard to know what you are going to get. But in my mind probably the biggest weakness of Arduino boards is that they are typically made using lead free solder, which is IMHO setting them up to die young. But the design of Arduinos seems to be reasonably solid and there is no reason I can think of to consider it unreliable or sleazy. The issues I'm aware of are all to do with manufacturing.
Having said that, a Classic Rev. 6 (for example) is not an Arduino. It's more an Arduino-like circuit, and really about the only thing it has in common with an Arduino is the Atmega328P controller. That and the fact that the code is written using the Arduino IDE and libraries and whatnot. But it's not an Arduino.
To design and scratch build, here are some things that come right to mind that you will need to do.
Design a high voltage power supply, preferably a boost converter topology, to power the tubes.
Design your display driving circuitry. Are you going to go multiplexed or direct drive? Traditional TTL decoder + transistors, or modern HV drivers (Supertex, etc.)?
Design timekeeping circuit. Traditional TTL or modern microcontroller? Which microcontroller: Atmega, PIC, ESP, ARM, the list goes on. Traditional TTL is more "vintage" (like the tubes) but implementing features beyond being a basic clock is quite difficult compared to adding some more code to a micro.
Decide what your timing source (determines accuracy) will be, and implement it. Plain old crystal oscillator, temperature controlled crystal oscillator, GPS, NTP via WiFi? Some combination of those? Crystal oscillators are probably good to a couple minutes a month, with a temperature controlled oscillator and patient "trimming" I've gotten as good as one minute a year, GPS keeps perfect time but your clock has to have a view of the sky, NTP is perfect as long as your clock has WiFi access. And so on.
Design the circuit board to hold everything together and see your board thru manufacturing. Or if you are very brave and crazy, hand wire the whole works on a perf board.
If using a microcontroller, program it. What language to use? Arduino toolchain, WinAVR toolchain, assembly language, ???
It's not a simple matter. I've never tracked the hours I spend on a new scratch-build (that's not just a mod of something I already designed once) but it's in the hundreds. Maybe Ian can chime in here and tell us how many hours he has into the design of his kits 0 I have no idea except that it will be "a bunch". Ian and I both have many years experience with this sort of thing and we both work in related fields.
TL;DR - I don't mean to discourage you but you should know what you are getting into! There is a lot to think about, know and do.
Look into it later when the dust is clearing off the crater.