The main disadvantage of low efficiency is energy loss. If you don't care about that, the booster can handle it, and the power supply can deliver the extra power required, then it's not important - to you.
All boosters have low efficiency at low power because they consume a fixed amount of 'quiescent' power which is not proportional to output power. Operating the booster in this region does not necessarily make it unstable, but it may have higher ripple currents and increased EMI due to running in 'discontinuous' mode.
A booster with low efficiency may also produce more EMI due to the higher current it requires. A 40% efficient booster needs double the current of an 80% efficient booster, and this current is drawn in pulses which tend to produce EMI. The higher current may also make the power supply voltage drop, causing the booster to draw even more current.
The energy consumed by the booster is wasted (mostly) as heat. If it can handle this then by definition it will not fail. However if running at high power it will get hotter than a more efficient booster, and so may have lower reliability and service life. You may not care about the waste heat, but the booster could care about the temperature rise it causes.