Labour depts conduct random checks and thats how the company may have escaped notice.
Also I wont always blame the employer in such a case, since even today I see plenty employees who would rather take a higher Take home than pay for their PF, ESIC, etc. Perhaps because they are unaware of their long term benefits or if they are 'Job-Hoppers' they anyway wont reap benefits of long term programs like Gratuity, etc.
However, since you are aware of this, you may volunteer information to relevant authorities if you feel like.
12th August 2016 From India, Mumbai