I have resorted to making a "Go pray you beardy mother f***ers" burrow to get around this, and usually I'll just lock everyone in it as a military alert for a couple weeks if focus is dropping due to lack of temple time. Even single-deity dwarves will often never go pray on their own if they work in a busy enough industry, I'm not sure if praying is just very low priority, or if they have to have "no job" for a bit before they'll do it. I use a similar "Everyone gets crammed into the same 3 room burrow" approach to socializing needs, since dwarves won't throw a party on their own anymore.
Multi-deity dwarves will work through their deity list in the order they're listed in the needs section if given a no specific diety temple from what I've seen, so they'll need a *lot* of down time to get through them all. Normally I don't bother and just let them be unfocused. The stress from the bad thought for not praying is usually not too bad, and if they get to pray to just one or two of them once in a while they seem to not fall below "Overall, <name> is unfocused by unmet needs" so they're not too heavily penalized.
As for temple... I usually designate a handful of meeting areas assigned as a single "No particular deity" temple complex, so there's always a nearby temple wherever my dwarf happens to be when they realize they don't have any real work to be doing. Temples to specific deities don't seem to be particularly worthwhile unless it is in response to a petition from that temple's followers (Or you just want to make them -- it can definitely be fun, sometimes Fun, and occasionally !!FUN!! to build thematically-appropriate temples for each of your fort's deities.)