(1) What is implied by "Underground water level varies from 5-6m" for the construction?
Typically this means that the groundwater table starts between 5m and 6m below grade. In other words, if you dig over 5m into the soil, you will likely hit the water table and have water in your excavation.
Construction sites use water mitigation strategies to deal with groundwater, which can be anything from using sump pumps to putting a slurry wall around the excavation. It all depends on the in situ condition and cost.
(2) What would be depth of typical base/foundation for an office complex building (3 stories, 50k sqm)?
Without knowing anything about the subsurface condition and what kind of equipment will be housed in the building, this question is really impossible to answer.
You could have bedrock 3m down. The soil could be cruddy organics or sand, which would require drilling piles down to a more stable soil strata. Your office building could house a heavy piece of equipment, requiring a special foundation.
Also, not knowing the footprint of the building makes it difficult to guess at a foundation design.
Does the underground water interfere in any way?
Groundwater pressure can make a building buoyant, which needs to be considered in design of the foundation.
You will likely have to include some kind of foundation drainage system into your building design to shed the groundwater away. Also, a sump pump system in the foundation will likely be needed, similar to what is done in residential basements.