Are these custom module Drupal tables lacking foreign keys? mysqldump with table structures without data is included
The answer is yes, they are lacking foreign keys, the previous dba was lacking all referential integrity and was using an application stage enforcement of the dba logic (as discussed here: http://dev.mysql.com/doc/refman/5.0/en/example-foreign-keys.html). The previous dba must have been inexperienced and possibly used this method:  


  For storage engines other than InnoDB, it is possible when defining a column to use a REFERENCES tbl_name(col_name) clause, which has no actual effect, and serves only as a memo or comment to you that the column which you are currently defining is intended to refer to a column in another table


However as me joining the project has proven - it is not necessarily a good way of doing it.

Given the sensitive nature of this project and the later desire to have all kinds of distributed systems accessing the db it has been decided that the overhead of having foreign key constraints is worth it for security when others may be programming and accessing the db. 

Whilst my comment on my question shows that it is possible for mysqldump to strip out important stuff and leave one with a misunderstanding, in this case there was no indexing and no foreign key relationships (someone else showed me, I will include how they found the answer if I can catch and get them to tell me).

From what I've been reading and seeing, Drupal does not really commonly use foreign keys, but that's another story altogether.