The caps should always be left closed when charging. Leaving them open won't do any harm as such, but it will probably increase the water consumption and allow small amounts of acid to escape on to the top of the battery. This will corrode the connections etc. The sites you know of which open the lids must be very small. The bigger sites i deal with have 80v batteries and these batteries are changed twice a day. To open and close 40 lids twice a day on 30 machines would be a full time job.