Yes, there are two options to make use of related objects.
For example, if we deduplicate accounts and want to make sure that the master record is an account that has active contracts then,
Option 1. Roll-up Field
Create a Roll-Up field on Account that will reflect status of the associated contracts. Then you can use this field in the rule that determines master record and prioritize based on it. More on prioritize rule here: Merge Rules: Prioritize by value
Option 2. Cross-Object Dataset
Create two datasets,
Dataset #1: Accounts with Active Contracts with the following SOQL Filter
Id in (SELECT AccountId from Contract WHERE Status = 'Active')
Dataset #2: Accounts without Active Contracts with the following SOQL Filter
Id not in (SELECT AccountId from Contract WHERE Status = 'Active')
Then, create a cross-object dataset where Parent is Dataset #1 and Child is Dataset #2.