I posted my question to the Inkscape subreddit after deciding I'd probably forget to check back here regularly, but I never found a solution on there. I'll just link you directly to the post since some discussion took place there:
https://www.reddit.com/r/Inkscape/comme ... eird_when/

Anyway, the issue is that when drawing, whether with a mouse or drawing tablet, strange chunks are missing from the lines. This is most obvious when drawing slowly or with sharp angles. I'm using settings very similar to the marker pen. The takeaway from my post on Reddit was to use a raster program such as GIMP instead, but if it wasn't for this issue Inkscape would be perfect for me, as I feel vectors are the way to go for simple line drawings. Please leave any suggestions as to why this issue may be occurring.

Hi.

Let's say using a mouse.
Gimp samples the route of your movements in even distances that you can set in the brush settings.
Whereas inkscape is hard-wired, it follows the movements of the cursor.
If that means very littly shifting in direction, it will be exaggerated. Try increase the smoothing settings =samples averaged more-, and/or add more weight to the calligraphy pen settings =so that the counter won't be that wonky of a subtle change in direction.

Using a tablet? More inputs that can alter the shape. Haven't tried it myself, guess pressure opacity can make the problem more legible.

Even with the calligraphy pen's mass set to 100 I get these issues. But increasing it a little certainly helps matters. I've just had a bit more discussion on Reddit and it does seem like there is no perfect solution and that may just be the nature of Inkscape. I'll play around with mass a bit more.