There are several factors with the HP IV being imperfect that may cause some problems.
Anything that takes out a specific percentage of health. Stuff like Life Orb, Rough Skin, Spiky Shield, Sand, Hail, Stealth Rock, Spikes, and Leech Seed will take off less of your health. As most of these residual damages take out the maximum amount of damage from even HP, an odd HP stat is beneficial. There are cases where Pokemon deliberately run lower HP IVs to minimize damage. Most Pokemon weak to Stealth Rock run an HP stat that isn't divisible by 4 (assuming they are only 2x weak to it), and sometimes, not divisible by 2 (Pokemon 4x weak to it). Cyndaquil is only 2x weak to SR, so it can afford to run a non-divisible number of 4.
Pokemon also lower HP EVs for Life Orb recoil. For example, Life Orb Latios runs 29 HP IVs in order to take 29 damage from Life Orb instead of 30. Pokemon's rounding down of everything is what causes this to happen.
As for something like Cyndaquil, it'll likely not care about a Life Orb, as Eruption is an asset that is dangerous at full health. Of course when you have lower HP IVs you'll probably take marginally more damage from attacks, weakening Eruption.
So of course it's better to have higher HP IVs, especially for a Pokemon who uses a move reliant on HP such as the Cyndaquil line. As people in the comments have said already, try for a higher HP IV Cyndaquil, if possible.
If not it's still viable! But sometimes an extra hit point means surviving something 100% of the time versus 99% of the time.