I work at a very similar place now that uses Shopify. Managing that many SKUs on Shopify is crazy painful.
The thing is is that custom ecom solutions really aren't that hard. The off-the-shelf ones are complex because, as stated above, they are trying to be everything to everybody.
I’m fairly confident I could spend a month or so writing a custom solution for a shop selling and shipping a few hundred tshirts a day that would save them enough money to break even on the software in a few years (compared to off the shelf solutions).
If I was starting my own tshirt company, I’d definitely do it.
We did an evaluation on several out of the box ecommerce solutions and none of them were able to meet the requirements that absolutely had to be there. Shopify flat out said no, they can't help us, etc.
I think we generally have this problem. It's not the typical business that can use that stuff, it's the average business. Unfortunately no business is the average business.
8 years ago we built our own ecommerce site + warehouse app (inventory tracking, fulfillment, receiving) for a few hundred orders per day. The goal was to be able to better see profit margins by product, track where the money was going/coming from in detail, along with cleaning up the inventory management part of the operation.
The warehouse people loved the change because it really streamlined the fulfillment process and it basically reduced their errors to zero. Owners loved it because of the all the cost/price tracking. It took about 6 months of work by 2 devs.
Before this they were on woocommerce. It was slow as shit. We looked at shopify but the integrations with 3rd party warehouse stuff was bad. The other solutions we looked at were overly complicated swiss army knives.
I'm going to take a wild ass guess here that you are wildly understating the "bit of legacy spaghetti"