Compounding frequency is the whole difference between the two numbers you see quoted. A 50% APR compounded daily becomes roughly 64.8% APY; at 100% APR it becomes about 171%. The quoted APY assumes the harvest keeps happening and the reward token holds its price.
Whether it pays depends on gas. Harvesting a $500 position on a chain charging $20 a time is value-destroying, which is why vaults batch harvests across all depositors and why optimal frequency falls as fees rise.
Be careful comparing advertised numbers. Protocols quote APR and APY inconsistently, and an APY figure derived from a reward token that has been falling all month is arithmetic detached from outcome. Convert everything to the same basis before judging.
Related: vault-strategy, yield-farming, real-yield, gas-fee