Physical device connection:
Nothing about KOReader or calibre will either cause or prevent your Kindle from connecting as a USB Mass Storage Device.
I am unsure how you check for detected physical devices -- on Linux I would run `dmesg` to see the kernel event log.
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Wireless Device connection:
If the problem is connecting as a wireless device, the first thing to check is, can you access the Content Server from the Kindle using the builtin browser?