Operators such as = are used with performing finds not find/replace. To use = to find a record with a blank field, you'd enter find mode, type an = in the field, then perform the find. This only searches on the field where you entered the operator so you'd have to do this once for each of you 100+ fields. Once you've found such a group of records, you can use replace field contents to put a 0 in this one field for all the records thus found.
You might want to craft a script to both find and update your fields to reduce the monotony involved.
With Find/Replace the finds search for example text and I can't see any way to use it to search for blank fields. If you are reading this and know of a way, please post as it would save a lot of effort here.
Yes, I figured "=" wasn't working in this case (as you said it only works during find mode), but I thought I would give it a shot.
I do know how to find/replace fields across multiple records using "replace field contents" but I figured there must be a way to do this for multiple fields within the same record.
It seems like such a simple thing, but I can't figure it out.
You might consider a script like this:
Go To Field [specify the first field in the layout's tab order]
Enter Find mode 
Insert Text ["="]
Set Error Capture [on]
perform Find 
If [ Get ( FoundCount ) > 0 ]
Replace Field Contents [no dialog ; "0"]
Go To Field [next]
Exit loop if [ Get ( ActiveFieldName ) = "name of first field in tab order"]
As with all trials using Replace Field Contents, make a back up copy first so you can toss the file and try again if it doesn't work the way you expected.