It really depends on what you're content is. Technical books with equations turn into garbage when I convert, and the formatting is all off. It's just easier to do PDF for me.
Have you tried the KindleUnpack plugin? [0] I originally used Calibre's built-in "convert" option, but I found I've gotten much better results from KindleUnpack. It gives a much "cleaner" EPUB with less of the annoying Calibre watermarking in the CSS and such.
To add, I used to keep my kindle not attached to an amazon account (so no email), but I plugged it into USB like a flash drive and synced books with Calibre.
Worked for me really well, it's great at bulk conversions. and I used to charge it on my desk anyways, so it wasn't much of a hassle to remember to sync.
There's also the excellent ebook-convert command line tool as part of Calibre which can be used to convert between the formats[1], I use it convert HN content to Kindle e-book for my https://hntokindle.com.
Rarely ever had a problem with that, it's just one additional step with emailing your kindle address with the book.