Schoolboy error; I just wanted to alter the layout of my military bunker base a little, but when I (eventually) went up to ground level I realised I had made big holes in the ceiling 
Is there any way I can repair this?
Furthermore, is there any way to remove parts of walls inside a bunker without the roof caving in?
Go downstairs again and use the construction menu (opened with *) to build any type of roof on the tile that has a hole in the floor above. That should fill in the gap.
Not anymore (assuming you’re playing on 0.F stable or newer), at least not that I’m aware of (mods aside).
Ok, I built a metal roof and I now have a metal roof tile where there used to be a hole! Two questions though: how can I get the soil layer back (I was farming there), and does it make any difference what material I use to build the ceiling, wrt intruders?
As far as I know, there are multiple ways to get the soil back. Still assuming you’re playing on 0.F+, the probably easiest/cheapest option is to construct Make Gravel Floor, followed by the Remove Gravel construction.
If this doesn’t work (it might has changed over the versions), you might want to use the Deconstruct Furniture on the gravel floor, which should leave a pit that you can fill in with a shovel.
Alternatively, you can use the Build Roof Over Dirt Floor… That requires adjacent (supporting) walls or roofs though, which takes a lot of material to construct.
No. As far as I’m aware, intruders – be it monsters or NPCs – can’t beat or dig through ceilings (yet).
Thank you, all fixed!
I used the gravel / deconstruct / fill in method (in 0.F) - needed 2500 pebbles though!
Hilariously, mobs can’t even see or move up/down Z-levels without a stairwell or ladder (or by dying and dropping their corpse to the ground). This is the only thing that makes my lab-fortress survivable… there are like 600 flaming eyes hovering around one Z-level up from the ground floor, and thankfully only occasionally do one or two bumble into a ladder or stairwell somewhere and become a problem.
Glad it worked! Luckily, pebbles are easy enough to come by, given that they can usually be found by digging pits somewhere. 
This isn’t accurate. Zombies that can jump (like hunters) actually do jump up (or down) buildings to attack you, and do/did since a long time ago (there was even a bug that caused them to jump through solid ground to get to you).
I’ve also had wasps decend from higher z-levels to attack my character.
However, to be able to experience this, the option for Experimental 3D vision has to be turned on. This might still lead to turrets underground targeting you and trying to shoot you through solid ground (hence the experimental part).
Yeah, I have enough trouble with bugs just playing the experimental versions, so I never turn on any other experimental features. Out of curiosity, though, does 3D vision give the player the ability to see into other Z-levels, too? I can only see other Z-levels in the overmap.
Yes.
It also allows them to aim and shoot at monsters on other Z-levels.
However, other than the turrets, the character usually* respects solid ground. So you can see down out of a window from an upper floor (or up through it from the outside), but you can’t see into a basement from the outside of a house.
*: On some rare occasions it can show you monster on your compass that you can’t really see.
I’ve been able to fire upwards at flying critters, but all my attempts at attacking downwards (from a roof or the top of a stair) have failed miserably. The missiles fired from a stair just hit the floor/top of the stair, while those fired from a roof just disappear (I’ve been using rocks and arrows, which SHOULD be recoverable much of the time).
