Pads will be inferred by the implementation tools if there are I/O bufferprimitives (IBUF, OBUF, OBUFT, etc.) in the logical netlist. To prevent the implementation tools from instantiating pads, the I/O buffer primitives need to be removed.
Contact the 3rd party provider of the encrypted netlist to check whether they can provide a netlist without I/O buffers. Typically, this can be done by turning off the "Add I/O Buffers" property for XST (Refer to Xilinx Answer 34771). 3rd party synthesizers have similar switches, which can be found in their documentation.