Yes, it had a lot of custom chips, and some of the same people (like Jay Miner) who worked on the Atari 800 design later were involved in designing the Amiga which likewise was based on custom chips.
there were 3 custom chips (ANTIC, GTIA and POKEY) 1 semi-custom (SALLY was a VERY MINOR modification of 6502) and 1 common industry chip (PIA). I would not say exactlly "lot of" ;-)
Well, relatively speaking that was a lot for late 1970s microcomputers. The original Apple ][ and TRS-80 Model I were essentially built from off the shelf chips (which is why both got off-brand clones).