They are, at first, both expensive and labour intensive. Furthermore, considering their importance, they are often built when resources and manpower are both in shortage which adds an additional hardship for the colonists. Despite this, it is a necissity as it mines the raw materials required in further development of the colony by producing processed goods that are then used by workers.
The Eta class is a flexible design that produces little waste but production is at a slow rate. This is why additional wings are added to the structure during one of the colonial upgrades. A total of six wings can be added to the facility, each of which enhances the efficiency of the structure.
There was a problem noted on two occassions with the design which was the account that fissionable material was both mined and stored in the specialist 'wings' while Deuterium was housed in the central mining hall. This meant that once ignited, the entire facility may be destroyed. (TOS video game: New Worlds)