Does Humility remove abilities granted by counters like the flying from Crystalline Giant?

Humility's effect reads: 'All creatures lose all abilities and have base power and toughness 1/1.' The keyword 'all abilities' means every ability a creature currently has, regardless of how it was granted — whether printed on the card, granted by an Aura, Equipment, or a counter.

When Crystalline Giant gets, say, a flying counter, that counter causes a continuous effect that grants the flying ability to the creature (CR 613.1). Humility's effect also operates in layer 6 (ability-removing effects) and strips away that granted flying ability. The counter remains on the creature, but the ability it would normally grant is suppressed while Humility is in effect.

This is because the flying counter doesn't 'store' the ability inside itself in a way that is immune to removal; it simply creates an ongoing grant. Humility's blanket removal overrides that grant in the same layer (layer 6), so the ability does not function (CR 613.1b, 613.6).

Example: Crystalline Giant has a flying counter and a trample counter on it. Humility enters the battlefield. The Giant becomes a 1/1 with no abilities — it loses both flying and trample, even though the counters are still physically on it. If Humility leaves the battlefield, flying and trample immediately return.

Note: the counters themselves are not removed; they are just temporarily doing nothing. Once Humility is gone, all the abilities those counters grant come back immediately.