I’m not sure where to group this. But when making scripts that add prefix or suffix to naming things. Do you get the user to add a space before or after and give them a hint to do that. Or do you add it in for them in the script. But by chance if there was a dot to start the suffix this would cause an issue… Have I answered my own question? 
Curious if anyone else has thoughts on this or am I over thinking it
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Depends on how rigid the standards are. Generally I’d get the user to include the prefix separator in the prefix for flexibility.
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Yes. If you’re really concerned trigger a pop up that shows the result (ie: {parameterVaueHere}.SuffixHere) and allows the user to cancel or send the value(s).
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I would let the user use a separator, but I would probably have a dummy value in place for the suffix so the user can see what kind of formatting is preferred (you might want an underscore instead of a space).
About dots and forbidden characters in the context of Dynamo you might check if the input contains such a character and show an error message instead of continuing with the script.
In the context of an app you can have a function that only allows certain charactes as input.
You haven’t given any specifics on whether this is a standardized naming convention or a flexible one. So it kinda depends.
In my experience, when dealing with standardized naming conventions that include a prefix and/or suffix, the separator is not part of the prefix/suffix. If the naming convention is already set and the separator is known, then the user should not be including it at all. If the naming convention is flexible and a specific separator can be provided, then it should be provided separately from the prefix/suffix.
As a side note, you can always include a check for duplicated separators to make sure users aren’t defining inputs improperly if you’re worried about that happening. But well defined inputs will always be better. @viktor_kuzev also makes a good point of using a placeholder or default value to prevent any issues there as well.