I'm looking to house hack and purchase a Section 8 Housing Duplex in Baltimore, MD. I would live in one unit and rent out the other unit to Section 8 tenants. My question is, is it legal to live in section 8 housing when I am not in the program but own the house? 

As long as its a real duplex.  I would email the city unless they have opened up the permit office down to confirm this.  If its the county you can check prior to buying at their office as well.  A valid rental license will note the unit #.  Confirm for yourself before buying.

Anna you seem to be mixing up Project Based Rental Assistance (PBRA) with the voucher scheme. The PBRA is for large apartment buildings where the owner has entered multi-year rental assistance agreements with HUD. PBRA stays with the unit. The voucher stays with the tentant.

When you say you have a section 8 duplex that is most likely a duplex with two voucher holders in there. These can be turned back to a private rental whenever because the voucher belongs to that tenant not that unit. 

Be sure to heed Tim's point. There are a lot of "duplexes" in Baltimore.