The viaCollections are the m:n relations. By default they're hidden, as configured by the preference "HideManyToManyRelationsOnCreation". This setting is true by default.
You can hide m:n relations in bulk with the plugin provided in the designer. Right click 'Entities' in project explorer and select the plugin from the 'run plugin' menu. There you can specify which entities to hide the m:n relations on.
There's an issue currently with the initial size of collections. The initial size is set to 32 references. This is small, though if you have a truckload of m:n relations in your entity, you'll get unnecessary memory consumption. This will be fixed in v2.1, a free upgrade for v2.0 users.