I will answer my own question as enough time and testing has now been done to give a correct answer. The answer is "Yes" it currently does hurt my SEO, however it doesn't have to. Let me explain.
At the moment the navigation includes many links which, though thematically connected in a hierarchy, are effectively seen as separate pages by google which stand alone. The combination of many links along with no thematic hierarchy or structure is causing a problem as it is massively diluting the themes of each section of the site.
This referential structure actually extends to all linking in the site but this is by far the worst offender. I hope this helps anyone else with a similar problem - if you want to understand this conclusion more I recommend reading into content siloing as it is an often misunderstood concept in SEO.