The absence of her mother is possibly remarked upon during the rehearsal dinner:
there is a brief mention of Phoebe's mother at the rehearsal dinner, and Phoebe is about to explain why she isn't there, but Monica keeps rushing her through her speech. (Although it's not entirely clear whether she means her birth mother or her adoptive mother.) Not sure if this was one of the deleted scenes that wasn't in the original airing.
(Note that IRL Teri Garr had been diagnosed with MS in the years before this episode, so that might explain why she wasn't in the episode.)
The most likely explanation is however that the Friends writers were awful at continuity and forgot about plenty of close family members of the characters for years (e.g. Ross's son etc.).