I figured out you can get around the 100-issue limit in the Jira automation Lookup Issues action by leveraging the {{lookupIssues.last}} value, specifically in this example lookupIssues.last.key but I imagine this could be adapted for other fields.
1. Do your JQL query in the Lookup Issues action.
2. Do whatever you want with the first 100 results.
3. Create variable action, call it myKey, set it to: {{if(equals(lookupIssues.size, 0), "outOfScopeKey", lookupIssues.last.key)}}. The placeholder outOfScopeKey is something you know won't return anything from the next JQL lookup. For example, if you're filtering for issues created in the last day, use a key you know is older than a day. If the lookup issues size is 0, the conditional logic will return the out-of-scope key, if anything else, will return the last key.
4. Repeat the JQL search, but add "and key < {{myKey}}". This will get up to the next 100 issues if there are over 100 issues in the first call and will return nothing otherwise.
This process can then be repeated as many times as you want!