Item 1 - Connector terminals are only auto-loaded in VeSys Harness, so creating a Circuit Data Export from VeSys Design would not include the information that you require.
Item 2 - This sounds like a defect, have you sent the data to SupportNet ?
The schematic in VeSys Design is just that a schematic and so it doesn't have much reporting in the way of detailed information such as Terminals, it also will not report wire seals, cavity plugs, tubes, tape coverings, clips or grommets because this level of information would be very hard to capture from a schematic drawing. It would be possible to write a macro to do terminal selection but it really depends on why you want the software to do this as the BOM will definately be short of a lot of components required for harness Manufacture.
Your second problem of having VeSys report both halves of a connector, I suspect this is related to an inline connector? If you are using a component connector then VeSys shouldn't auto-populate the opposing connector, the option you are picking to select 'show male' or 'show female' is only the graphical representation of an inline connector.
Further to my previous post you could always use a custom component as this doesn't auto-populate both halves of the connector and doesn't report on them.