I think a natural choice is large provides like Amazon.

However, if you want to sell eBooks on your own and maintain all of the revenue, then WooCommerce and Easy Digital Downloads would make excellent options.

Both software packages are WordPress plugins and they make it very easy to deploy an e-commerce store for digital goods.

Both plugins have strong development teams behind them and they have a slew of independent freelancers who can offer assistance if needed.

I've used WooCommerce myself for multiple years and we've deployed many WordPress websites that use it. It has hundreds of extensions you can add on to it for maximizing the potential.

I have had over 5 years of experience helping clients in Africa to publish their content in various format and I have sound knowledge of e-commerce stores.
This is an interesting question because there are thousands of ways or methods to use to fulfil this singular project. In order to help you derive an answer to aid your decision making, I will ask you: 'What is your main goal or objective for an e-bookstore site?'. Are you looking at scope of distribution- reach? Are you looking at purchase fulfilment?
Your 'process' of achieving the desired objective should be your least concern. If ever you will be concerned about the platform to use then your concerns should border on cost, security, reliability, availability, etc.
If I was the one setting up an e-bookstore, my main concerns would be: 1. Distribution scope - in which case I will be looking for a platform that would afford my ebooks or content the widest reach possible. An in that case, I will be looking in the direction of Amazon platforms. Amazon has a wide reach and there is no need my reinventing another wheel in this regard.
In terms of relaibility, security, availability, etc the Amazon platforms have it.
Shopify is also a good platform and should get you up and running fast. If you would resort to WooCommerce , then your costs of development might shoot up since you might need a developer services to help you integrate the WooCommerce plugins(otherwise you might estimate the cost of time you employ going the DIY route). When you sum up the costs, then going the Shopify route is preferable seeing Shopify already has DIY tools that can easily get you started. Compared to Shopify, I personally think BigCommerce is more affordable(this might be arguable).
In summarizing, there is no need building from the scratch since that means 'reinventing the wheel' plus its attendant costs so going the Shopify/Amazon/BigCommerce route seems better.
Back to my Scope of Distribution factor which is key to the success of online e-book distribution, (after all, you aim for an e-bookstore is not charity but for making profit), you might as well explore the 'new marketplaces' such as hosting and distributing your ebook content via Googleplay, iTunes and Amazon stores since these are already have huge 'viewership'. That means you can distribute your ebooks in 'app' formats or pdfs.
Your end goal should be to make ROI of your investments.

The better question is: what will make your online bookstore stand out from the others, especially big boys like Amazon? If all you want to do is sell books, use Amazon's platform as a network seller.

What in your business plan makes you unique enough to edge out a niche in a crowded market? If you're interested, we can discuss this further.

The problem with many eCommerce platforms, including the ones you mentioned, is that they were designed for micro-businesses. They are not aimed at businesses that are growing quickly and taking advantage of modern tactics.

This is great for getting started, but not great if you have ambitions to grow the business long term.

That's why we developed LemonStand. We offer a platform for the next generation of entrepreneurs that need flexibility and features to help them innovate and grow quickly.

You can check us out at https://lemonstand.com or schedule a call with me to specifically discuss your project in depth.

Best,