Esi short deduction

No, those employees earning more than Rs. 21000 (excluding over time allownce) per month will/can not be covered/registered under ESIC.
At present wage ceiling in esic is rs 21000 per month, I.e., only work force getting wages less than 21000 should be covered under Esic

Vinod Ji this is not my question. First you again read the question then answer the same.

Pay balance ESI with interest and penalty

Rate of interedt
Sub-Section (5) of Section 39 of the ESI Act 1948
Employer shall be liable to pay simple interest @ 12% per annum or at such higher rate as may be specified in the Regulations, till the date of its actual payment.

Penalty
# No.of days delayed in making payment x 5% p.a (Less than 2 months)
# No.of days delayed in making payment x 10% p.a (2 months and above but less than 4 months)
# No.of days delayed in making payment x 15% p.a (4 months and above but less than 6 months)
# No.of days delayed in making payment x 25% p.a (6 months and above)

I did not fully understand your query. Are u asking whether to deduct esi or not for employee salary more than 21000.

Sorry Vinod Ji.. I want to ask that todays limit of ESI is 21000 but my company deduct only those employees whose salary less than 15000. So whether company liable for the same. if yes so what the liability on company accrued.

The company is liable to pay the contribution amount of all those exclude employee's salary between 15000-21000. Any way pay the arrears contributions currently.
Later You will receive Interest and damages notice by Esic department. After that, you can pay it.