Yes, these are known problems. I'm not sure if they are considered bugs.... Actually I reported most of those, although the report has not received any attention from developers yet. Let's see if I can find it....
https://bugs.launchpad.net/inkscape/+bug/1449815 It seems to me I first saw it happening in version 0.91. But when I was testing, I found it happened in 0.48 too. Maybe I just didn't notice it then, but it seems to be getting worse for me.
But yeah, those problems make me bonkers too! It happens with more things too, besides just the booleans. Paint Bucket, Trace Bitmap, LPEs (spiro spline is the worst, for me) anything where you need Object to Path, etc.
In some cases, Path menu > Simplify can reduce the extra nodes. But you can't just simplify the whole drawing at once. It works better to do it one path at a time. Or you can do it a few at a time, if the paths have a similar number of nodes.
Proactively....it seems like I remember someone suggesting to use Edit menu > Inkscape Preferences > Input/Output > SVG Output > Path Data, set to Absolute. But don't quote me on that. I have NOT tried it. (I'm set to Optimized). (This problem was happening before that option was created.)
Lazur's suggestion is definitely worth a try though.