It's been a while since you asked but I had the same problem and got to the bottom of it.
$ sudo rm /etc/fonts/conf.d/60-droid-sans-mono-fonts.conf (this is just a symlink so no actual configuration files are lost).
ttf-droid got replaced by
fonts-droid. With that the symlink
60-ttf-droid-sans-mono-fonts.conf in the folder /etc/fonts/conf.d/ got renamed to
60-droid-sans-mono-fonts.conf. That means that the configuration in that file is now read before all configuration in
60-latin.conf and thus overriding it. The font alias Monospace (which is used by default in Yakuake and Kate) is defined as alias to DejaVu Sans Mono in 60-latin.conf, but Droid Sans Mono in 60-droid-sans-mono-fonts.conf. Incidentally, that font does not have a bold version, at least not the files in the fonts-droid package. So everywhere where Yakuake and Kate are supposed to render bold letters the rendering falls back to the regular version of the font.
If you do not want to change the setting system wide you could instead add your own alias to Monospace in ~/.fonts.conf. This should work:
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<family>DejaVu Sans Mono</family>
You can take a look at all the files in /etc/fonts/conf.avail and the fonts.conf manpage to see what else you can put into your .fonts.conf.