The Ricoh 2A03 (NTSC) and 2A07 (PAL) are best thought of as ASIC devices. They include a 6502-compatible CPU core, but these chips also include the NES's 5-voice Programmable Sound Generator. The inclusion of the PSG, plus other I/O interfaces for the NES, together resulted in 22 internal memory-mapped I/O ports that are on-chip. As you mentioned, the binary-coded decimal instructions were disabled too.
The BCD functionality of the 6502 was not useful for the NES, since there was no requirement to interface to a 7-segment display. The main reason for removing the functionality was probably to avoid any licensing or royalty issues related to U.S. Patent 3991307 held by MOS at the time.
The Ricoh 2A03/2A07 ASIC, together with the Ricoh Picture Processing Unit chip, comprise most of the necessary electronics for the NES by covering CPU, graphics display, controller inputs, and sound generation.