Shopify takes deceptive practices very seriously and expects that every Shopify merchant shall act with integrity and in the best interest of the users.
As you said nothing on the website was deceptive, you might be referring to the products or services offered through the website.
The problem can be in the code, like:
Obfuscating the code: Changing the simple code into a complex one, which becomes difficult for the search engine crawlers to understand. These codes do not fulfill their actual purpose but confuse the crawlers, and fulfill the hidden purpose. It can hamper the user experience on the website.
Cloaking: It is the practice, where the code presents different content to the search engine crawlers than the users. It is aimed at ranking higher by increasing the keyword density and improving page SEO score.
Both the mentioned practices are black hat SEO practices, which are intended to deceive the search engines. These practices help the website to rank better on SERP, and hamper the ranking of the websites that actually have good-quality content; thus, such practices negatively impact the user experiences on the website.
You can contact the Shopify help center to get further support and get the store back.