I personally haven't used the .NET SDK but I've used Enigma a few times to extend Qlik functionality. Both options are essentially wrappers around the Qlik Engine JSON API and provide Qlik objects as language structures. For example, the Qlik Engine API includes a Hypercube structure which the .NET SDK includes as the Hypercube .NET class and that Enigma.js includes as the Hypercube JavaScript object.
The .NET SDK also provides client options for rendering Qlik visualizations inside of your custom Windows solution (like this example from the Qlik Help site). Though Enigma.js does not offer visualization rendering APIs (since it's Qlik Engine only), you can use it along with Qlik's Nebula.js JavaScript library to render visualizations.
Both projects are very well-maintained and updated by Qlik. You can see the .NET SDK stats on its NuGet page and Engima.js's stats on its NPM page.
So ultimately, you can do the same sort of things with either project. It all comes down to what sort of things you want to build and what tech stack you/your team is most comfortable with. If you're already familiar with the .NET/C# ecosystem and language, you should probably go that route, especially if you want to create custom Windows apps/GUIs. On the other hand, if you're wanting to get some "quick wins" and are comfortable writing JavaScript, you may want to go with Enigma, especially since Qlik has been making more significant progress in that space recently and shares a lot of new examples using Enigma on its qlik.dev site. You're also able to use TypeScript with Engima.js, so you wouldn't be losing out on type safety, if that's important to you. And modern tools like Electron let you create really solid desktop apps using JavaScript/TypeScript.
