There's really nothing to worry about.
Shindo has been in business (as Shindo Laboratory) since 1977. Which means that only a handful of companies are older. They have been 'writing the book for decades'. I think people get an impression that Shindo is new because they only started hearing about Shindo the last few years in the US. Shindo is a small operation but is not a one man operation. One of Shindo's sons has been working at the company and probably will take over someday.
If you check out Japanese used gear sites, you'll find an occasion older Shindo gear for sale including the earliest stuff that comes in brown. (The early Shindo gear was brown). All of these units still work perfectly. I've seen and hear many older Shindo gear that have been sent back for tune-ups, repair, adjustments and have returned better than ever. One of the cool things about Shindo is that he keeps a supply of parts and tubes for all of the gear he has sold.
The second point is that Shindo tunes each piece to a specific sound. He can get the same sound using slightly different tubes and parts. I have a Vosne Romanee preamp and my friend has one too (about 5 months difference between the two units). The phono stage tubes between our two units are not the same but the two units sound the same. We are not talking about different brands of tubes but totally different type and electrical characteristics. No matter what the parts situation, Shindo will be able to get a piece of gear working again.
I built my own tube gear for 15 years. I went to an all-Shindo system because Shindo is a legend among the DIY crowd. His layouts remind me of the way Tektronix used to layout all of their oscilloscopes. Very clean, efficient, and easy to work on. In contrast, I've seen gear made by many domestic companies including some that have been around for decades and the wiring quality, layout and design could best be described as being wired by "crazed monkeys". (A term one dealer used to describe the insides of a piece brought in for repairs).
The prospects of having to send your gear back to Japan for repairs might seem daunting. But shipping to Japan is easy. I've sent things to Shindo and received things from them and the transit time is usually less than 7 days. I buy a lot of stuff from Japan especially fountain pens and shipping via EMS is fast, relatively cheap, and easy. I've had one problem with my system and that was a freak problem with my Shindo cartridge (my fault). I gave it to Matt at Pitch Perfect and he sent it off to Shindo. Matt lent my a loaner cartidge to use while mine was being repaired. It came back a few weeks later at no charge. That's about as good as service you will likely find. The temptation is often to buy used. But in the case of Shindo, the service from the dealers like Matt and Jonathan the distributor is worth the extra price.
Just because a company is based locally doesn't mean repair work will be easy. I've been in audio for about two decades and have seen enough complaints of gear sent back for repair a few states away and either come back not repaired properly, come back at the turn of the next century, or are not capable of being repaired at all. As for NOS parts, I'd would trust my life to a 50 year old capacitor made by Western Electric rather than the latest boutique capacitor in many pieces of modern gear.
When I bought my first Shindo piece about three years ago, issues of service never crossed my mind. When I would receive my preamp was probably at the top of my mind. Three years later, I have a system that is all-Shindo from cartridge to speakers (cables, power conditioner, ...everything). I paid for all of it. I don't think problems of service every cross my mind nor do they haunt my sleep.
These thoughts are based on my experience and your own experience may differ. I'm certainly not going to say every piece will always be perfect and things do happen. However, I don't think getting something repaired will be an adventure. You may have to wait a bit but things will turn out.