After finally deciding to try my hand at Skyrim modding I was thrilled (yes, heavy sarcasm here) to find out that my favorite house and Heartfires simply do not get along. In order to prevent me from further frustrations I would like to ask any kind souls to tell me, if this bug happens to be in any of the other vanilla houses for sale, or if they are safe for modding and navmesh changes.

Thank you in advance for your advice.

It's only Breezehome. I had the same problem. I deleted my edited Breezehome navmesh and returned to the origional hearthfire/Breezehome navmesh and the crashes stopped. See this thread.
http://www.gamesas.com/topic/1456014-undoing-navmesh-change/

I used Balok's method using the CK.

It's good to know I am free to mess around with the other houses without repercussions (or at least CTDs). Unfortunately, just returning to the original navmesh for Breezhome wouldn't work - I have done some major reconstructions on the inside, so the NPCs would literally bash their heads into walls in it . At least I don't have to fear the same for my second favorite the Honeyside and can happily mod away in it. Thanks!

Remove your mod's navmesh edits. Save your cleaned mod. Start up CK and set both Syrim and Hearthfire as masters for your mod and save again. You should be able to now change your navmesh to suit without further crashes.

Will try this, thanks!

Crossi is right, that will work. However, many people do not want to make their mods dependent on Hearthfire for all users. There are two alternatives. You can turn your mod into an ESM (which stops the crashing, but I am not sure the navmesh will function for your modifications) or you can create a patch for it that just fixes the Hearthfire navmesh in Breezehome. The patch would need to be dependent on Hearthfires,esm as a master, but your actual mod wouldn't.