Is the bone in this case an aspect counting against the complexity deficit?
Not necessarily, but it absolutely can be. I would ask if it is more than just a symbolic link to the ghost. For example, if it was a ghost of a woman that was killed on her wedding day, and the finger bone was of her ring finger, the same that wore her wedding band when she was killed.
Now that's a fact that would definitely be worth an aspect.
I think a good rule of thumb would be to think how much space you'd spend on it in a novel. Half a sentence? That's just a symbolic link. A paragraph or two? Definitely an aspect worth tagging.
Another thing - the various ways of making up the deficit are all "montage" or "gloss over" things - the Declarations option can be a few quick rolls of Investigation, Resources and Discipline and you briefly describe how your character takes to time to Study Maps of the Area, gone out and bought a Silver Bowl to pour water in and Meditated, and that's +6 complexity taken care of for your scrying spell.
I agree with Taran, those sound more like they would fit to balance out the control roll than to aid towards the complexity of the spell.
The silver bowl could aid to the complexity, if it actually plays a part in the ritual.
The map is a bit of a weird one. Magic doesn't necessarily know how to read a map. It takes a more direct route than that. You could 'teach' your spell to read the map, for example. That could be a minor spell beforehand, or you have an item that can translate streetmap do magic for tracking spells. Just laying down a map isn't much of a help. Though maybe, if you are doing a Harry type tracking spell, and you have to check every now and again, you don't repeat the ritual every time, knowing the map is helping you to keep track of where you're going.
Meditation is a bit of a weird one. I feel like it is not a very inspired thing to do for a bonus. Sure, meditating to clear your mind for the spell is a common thing to do, but unless you actually have something to clear your mind from, I don't think it should have much of an impact. So I think this makes most sense when removing an existing aspect that could be used against you in the ritual, rather than actually creating an aspect.
Unless maybe you are doing something like Harry, when he imagines his circle to do thaumaturgy. But I think the "novel rule" from above applies here, too.
But what about stuff that I don't really see a roll for - like doing the ritual in a specific place (significant for the spell, but not a place of power) or at a specific time? Gathering grave dirt for the above ghost summoning? These must be able to contribute to the complexity, how do you handle them?
Either that is already an established fact from way before, and you just didn't get to use it, so you might already have a free tag on it, it just didn't matter up until now. Or you will have to spend a fate point on it, in order to make it matter.
On the other hand, how do you know to do the ritual at that place? Or the specific time? Or the specific grave to take the dirt from.
All those could be results of an investigation scene. Or a scene sneaking onto the cemetery to get the dirt. Or simply an investigation roll, if you don't want to spend too much time on it. Again, I would apply the "novel rule" to see if things are important enough to include them. Sometimes it is absolutely ok to just grant the player an aspect with a free tag, if they can tell a cool story around what they want to happen.
All the little details don't have to be single aspects, too. Maybe the place only works at the right time, so "right place and right time" would be one aspect, not two.