2n3904 SMD SOT 23 issues

Not so much.
Since 1988-2005 we were assembling our products ourself and we always were trying to have as small elements list as possible (not because of software problems but because of number of drawers to store them). So for example I had in my PCB program only the resistor values we used before and using any new value always was a decision if it is really needed.
When we started to order at contract manufacturer I stop being so restricted in element lists as it became not my drawers number problem but their :slight_smile:
When 2 years ago I decided to move from Protel to KiCad I found having about 400 symbols from which I decided that about 200 are ‘must have’ in KiCad and others “will add when will be needed”.
Now my KiCad SchLib directory is 134kB and my PcbLib is 404kB. Together less then one typical jpg photo. Till now I have defined only few KiCad PCBs using only elements from my libraries. I suppose they will be may be 2 or 3 times bigger in near few years as I think most typical elements I use I already have.
I don’t think it is very bloated library.