Problem seems to be solved!
Thanks to everyone for your input. Sorry I haven't replied to anyone yet, I've been a bit preoccupied ever since I bought XCOM and Dishonored on the same day.

do you have any mods that alter navmesh in Breezhome? I have read that Hearthfire causes Breezhome CTD if you do.
Did you have any mods that altered Honeyside?
Can you tell me what mods you were running? For a while I thought Smakit's Map Markers or Whiterun Breezehome - Breezehome Basemant from the Steam workshop were conflicting, but I've loaded my save up with no mods at all and the problem persists. Wondering if some mod may have made an errant alteration to my save data.
I'm running a sh#t-load of mods; specifically for Breezehome:- Breezehome Light Fix - to fix those stripy shadows. Breezehome Ladder Fix - stops you getting stuck at the top of the ladder.
I don't think I have any that directly affect Honeyside.
In response to people's suggestions, I disabled some mods one at a time. The Unofficial Patch had no effect. To my surprise, it was the Ladder Fix mod that did it! I then travelled from Breezehome to Honeyside and checked the cellar; it was fixed too! I don't know how this mod can affect two houses, but apparently it does. Kind of annoying; I hate getting caught at the top of those stairs.
Anyway, if other people have the Breezehome CTD problem, I hope this helps.