Flying monsters can, of course, bypass spike growth without issue, and the main weakness of Silence is that the zone doesn't move so dudes can just walk out of it if there's nothing stopping them from doing so.Beyond that, if there are trees or buildings nearby, the monsters can try to climb to avoid the spikes, or just try to jump over them. Depending on their position and ability scores, though, this might not be a good option.
Another good option is to throw down something to use as a stepping stone. A large rock, or a dead body, for instance. I recall that when I was DMing PotA, some particularly evil cultists actually threw their own mooks into the spikes to make a path for the others.
Another trick specific to Earth cultists would be to give one of them Move Earth. Target the area of the Spike Growth and have the spell level out the terrain, effectively cancelling it. Counterspell is also a very good (if a bit cheap) spell to guard against casters.
As for Silence, the best counter is to just have mooks with ranged weapons to support the casters. One trick might also be to have one or more of the monsters actually pick up the casters and physically hurl them out of the zone. This especially works with brutes like Minotaurs and Earth Elementals, who would have more than enough strength to toss a puny human.
EDIT: Also, yes, you're definitely within your rights to say the cultists can start scrying on the party or using divination magic to discover their common strategies. Spellcasting monsters would be dumb not to do this if they have the means. Not to mention that, IIRC each cult has ample opportunity to hear about the adventurers foiling their plans, and make preparations to deal with them.
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