For outdoors applications, you can get waterproof loudspeaker covers. These are used on PA systems etc. They are made to let the sound through without letting water in.
For your desk, covering the loudspeakers isn't enough. Your computer screen and keyboard also suffer when sprayed with fruit sap.
Loudspeakers do not need to be protected against dust, so they don't need to be covered full time, just when you are eating. This means you can remove the plastic bags after you're done eating.
Alternatively, stop eating at your desk. You need to get up regularly anyway to stretch your legs, use eating as another reason to spend a few minutes away from your desk, walking around, resting your eyes by focusing at a different distance, etc.
Your fear of headphones is unfounded. Just like loudspeakers, you are in control of the volume, and it's easy enough to keep the volume at a safe level. Headphones actually allow you to listen at lower volumes than loudspeakers, because headphones reduce the amount of background noise. Headphones also have the benefit that they don't disturb your colleagues.