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Those black dots look like magnesium deficiency to me. The yellowing of old growth usually indicates nitrogen deficiency, but yellow on new growth would generally be potassium. I think those holes in the lily pads are manganese, but I'm less sure on that one.

Can you list out what is in your fertilizer (macros and micros), what your nitrates are testing at and what your water change schedule looks like?

Also remember lilies have food in the bilb that will last quite a while, so they wont show deficiency for months, then, IME, when the stored nutrients run out they just sort of run downhill almost overnight.
 
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