Is there a way to block search for unregistered pages with toc?

Try duplicating your TOC. In one you point to one version of the TOC and in the other you point to the other topic. It's a nuisance having to maintain two TOCs but you may find it easier.

The better way is to apply two condition tags, different ones to each of the duplicated topics. Then create different expressions that you apply in the preset. One will exclude one version of the topic and the other will exclude the other version. Maybe create two presets so that you don't have to remember to change the expression.

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My site www.grainge.org includes many free Authoring and RoboHelp resources that may be of help.

I think that setting would mean the topic wouldn't be included in the search for the other output either, though.

If the reports don't provide some way of locating the links I suspect you'll have to go through each topic one by one, unfortunately.

Assuming the target is in the project, the link will pull it into the output and it will be searchable. I don't have access to RoboHelp but in topic properties I think there is an Exclude from Search. 

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My site www.grainge.org includes many free Authoring and RoboHelp resources that may be of help.

Hmm, is the problem that because they are linked, they are being pulled in to your output? I understood that wouldn't happen in the new UI, but it does seem to happen in a test project in RH2019 New UI. I'll tag @Peter Grainge in case he knows if this is expected or if there is a setting that controls it (the only setting I could find was only in the "print" output presets, not the "web" ones).

There are a bunch of reports in RH. I don't think any does what you need, but perhaps you can compare the data in a couple to figure out which topics need to be adjusted. You might start with the Topic List, Table of Contents and Topic References reports. I don't know if you'll be able to determine what you want, but that's were I'd start.,

I'm not sure I understand what you are asking. If you are using different toc files for each output, the search will only return topics included in the toc for the specific output. If you are using one toc but are excluding content using condition tags, then you will not see any topics that are excluded for that output.

If this doesn't answer your question, could you provide more information about how you have your project set up, what you are seeing and what you expect to see?