It's questionable whether there's any health issues associated with pyramiding or whether it's a normal process that occurs in tortoises when kept in hot and dry conditions.
We have, in our own breeding groups of Leopards, high pyramided females which produce regular clutches of eggs - which is normally only associated with healthy individuals.
Most species of animals that are kept incorrectly in captivity show signs of stress and become ill or die, whereas tortoises adapt to this change in environmental conditions by pyramiding to expand there overall surface area, to aid the absorption of what little moisture there may be in the air. The more extreme the dry air is, the more they will pyramid.
If a tortoise has started pyramiding as a juvenile, by changing its environmental conditions the pyramiding growth will stop, but will remain as it is and will continue to grow normally. If condition change once again to extremely dry at any stage whilst growing before reaching adult size then the pyramiding will start again.
Other shell deformities tend to be genetic, diet or incubation temperature related. Some babies hatch with extra or missshaped scutes. This tends to be an incubation issue, mainly being incubated at the top end of the scale of temperature limits. These individuals tend to be females as sex is temperature related, females at the higher end, males at the lower end and mixed sexes incubated mid-range. No evidence of health issues with extra or missshaped scutes.
Genetics plays a part in all living creatures and, from time to time certain males and females breeding together genetically may be incompatible and produce deformed individuals, rarely more than one within a whole clutch will be produced deformed and the rest will be fine.
Diet can play a big part in growth deformities, a lack of variations , calcium and multivitamin in the diet can have profound effects on the longterm health of a tortoise. The main key is to not allow your tortoise to feed solely on one thing, just because it's easy to feed or the tortoise tends to prefer it to anything else. Variety is the key to success. Always check the diet your species of tortoise should be eating as it can vary between species.