How do genealogical numbering systems (e.g. Henry system https://en.wikipedia.org/wiki/Genealogical_numbering_systems#Henry_System) deal with pedigree collapse? For example when marriage is between cousins or between person and her uncle, do their descendants have double numbers? Or what?
The recognized numbering systems were developed for the purpose of tracking individuals in published reports. With modern genealogy software, genealogists can generate reports without worrying about implementing the particular rules, or about re-numbering when individuals are added to the database.
How a numbering system deals with duplicate lines depends on the system and what options may be available in the software. In the days before computers, saving space (paper) and avoiding confusion were factors. Generally, the lower assigned number is the only line that is followed; however, there may be a cross-reference.
Ahnentafel (ancestor lists) - Published Ahnentafels will cross-reference the lower number when an individual re-appears in the lists. Genealogy software may give the option to hide or show duplicate individuals (especially in a pedigree chart).
NGSQ (descendant report) - all descendants are numbered both sequentially within the family and sequentially over the whole report; descendants with further descendants are identified by "+". When 2 descendants marry (each with an assigned 2nd number and +), their family is reported at the lower number only.
Register (descendant report) - all children are numbered sequentially within the family but only those with further descendants have a 2nd number that is applied sequentially over the whole report. When 2 descendants marry (each with an assigned 2nd number), their family is reported at the lower number only, but a cross-reference is shown beside the higher number, pointing to the lower number.
Henry (descendant report) - Individuals are identified by generation and sequentially within the family. My program doesn't have this report, but does have the similar Outline Descendant report, in which duplicate individuals are repeated and cross-referenced.
No examples shown, because reports with these marriages tend to be very long.
[The following was taken from my responses to the thread "Ahnentafel numbering problem" in the Ancestry Message Board "Genealogical Numbering System"]
People use genealogical numbering systems for a variety of purposes: publication (reports with ancestor numbering or descendant numbering), organizing source documents & images with linkage to individuals or families, identifying individuals by lineage or relationship. These are the main reasons, but there probably are others. Some systems are better-suited to a particular purpose than others.