In commercial and industrial situations, multiple circuits are allowed, and most electricians do it. They are careful to follow the rules on how many wires/circuits in a given size of conduit. For example, a 1/2" conduit can only have so many individual wires in it, wire size not withstanding (within reason). That is one of the considerations you will have to deal with.

Another consideration is that rules for pool electrical installations are quite often very different from and in addition to commercial/industrial/residential rules because of the more hazardous location an the inclusion of water in the mix. PoolDoc is advising you correctly to check the NEC for the added rules pertaining to pools.

As he stated, best would be a sub panel at the equipment area, with individual conduit runs per circuit. Stray currents/voltages in a pool setting have the potential to negate the use of GFCI's on the individual circuits, due to induction between conductors. GFCI's work by monitoring the voltage/current in the individual conductors of each circuit they are attached to. They may not sense the differences from interference from other circuit runs in the same conduit. If they do, both circuit breakers should trip, but don't always, leading to shock hazards you may not be aware of.