I have an emerald cut aquamarine that seemed much, much bluer when I bought it. I know aquamarines are pale blue in color or often almost white. If this stone was irradiated, is it paler because it's losing its color? Do they lose color or is the irradiation permanent?
Yes, there are aquamarine that have been irradiated to look a darker blue. This treatment is not stable nor permanent, so expect aquamarine treated as such to fade over time.
Blue topaz is treated, but unlikely to fade - if your stone is paler now than when you purchased it, and you haven't been cooking it deliberately, it's probably not topaz.
It's certainly possible to get darker blue untreated aquamarine, it's just rarer and more expensive, but yes, the irradiated material fades. It's quite commonly heated, but as far as I know that's not to deepen the colour, only to remove green hues, and it's permanent. Sorry to hear yours is fading!