The answer really depends on if you have any requirements from your customer or your company. If you don't have any clear requirements, I would think the annotations should be visible so someone else could read them without having to hunt for them.
I opened in the past assembly which contain many parts with FTA... I could not actually read any as they were on top of each other and I could not see the geometry because there was way too many FTA around...
If I had my way I would keep them in show but i will have them in some known layers so I can quickly remove them from the 3D with a visualization filter without actually modifying the files.
There are pros and cons in every situation ask yourself your constraints, your wishes, your options.... then make a wise choice.
do you understand my previous post now?
Eric N. indocti discant et ament meminisse periti
Yes, I understand.
Let's say you'd put them in layers. What'd be the next scenario?
Making that particular layer invisible?
How would the future users access them, if neccessary?
Annotations can be also manipulated with macros but really depends on what you want (hide all of them in one shut, hide a specific part which has annotations in a user selection a.s.o.).
Eric and MarkAF are right in what they told about working with layers, in some cases is really good to use them but this should be a way of work company procedure from the very beginning. If is done later on, is additional work/time.
I would keep them in no show. Create captures to show them depending on the set of FTA that you want to show common to one type of geometry in your model. It's my preference and a nice way to keep the model clean. Sometimes I'll show them, but I won't have the annotation follow the camera or anything like that as it will clutter up the model look. I lock them to planes & keep them small and oriented in a way that is logical and dressed out.
Create a capture that has All Annotations, Then a few Captures showing only certain annotations at a time & views that are appropriate and clean for those annotations, then create a No Annotation or Engineering Only Capture that you keep the part saved in.