Access_method just tells Data Pump how to load or unload data. It does not change anything related to metadata. Post your command and I'll take a look to see if there is something else in there that would cause metadata to change.
Your export command is excluding some tables. Since you said to exclude these tables, the dependent objects will not be exported either. Can you tell us what tables the missing indexes and constraints are on, and can you tell us which tables are in your exclude table list? If they are the same, then the exclude is removing them. When you say exclude=table, then any path with 'TABLE' in the path will be excluded. If all you wanted to do was exclude the table, then you need to be more specific. Here is an example:
If you say exclude=table ... then all of these will be excluded.