You can use a low frequency DC-DC with slow controlled edges or sine, but the required iron-core transformer is bigger. I don't know nanocrystaline transformers are out there yet, compared to ferrites. I've used little audio transformers, but not sure of your isolation voltage requirements - galvanic or mains?
Higher freq. say 100-500kHz is compact off-the-shelf modules but as you say much harder to pass stringent EMC. The little 1W converters are convenient but very noisy and you lose any benefits from all the extra filtering you have to add, and then they still radiate enough to warrant a metal shield.
For conducted emissions, the transformer's primary-secondary winding capacitance couples your two isolation sides at RF. So EMI on the primary side can walk out the secondary side. You must use a CM choke and Y-caps on the output of the DC-DC. It depends on your product's noise sources, i.e. a GHz CPU making the primary side power dirty can surprise you radiating GHz emissions out on your galvanic circuits and associated field wiring.
So I'd use a soft/resonant/Royter push-pull DC-DC, with say 6VDC or so unregulated output and CM filtering, then LDO to make quiet 5V.