Section 11 B of Central Excise Act, 1944 is meant for both duty and interest paid.
Since you paid duty under protest, it is clear that you had not paid interest. You want to claim interest because your money was locked up in Court case. It remained in the custody of Central govt. for about 18 years. You suffered loss of interest for a considerable period. When any amount is locked up in a court case, it depends upon the nature of decision of the Court under what form consequential relief is to be given. You should have taken up this issue at the time of filing writ petition with the Supreme Court i.e. at the initial stage. Normally, in such a situation, especially, in the absence of any claim in the main appeal, interest is not paid.
However, there is no harm in fighting the case for interest. Why you should suffer without any fault of yours ? Why Govt. should be enriched by way of retaining money (without interest ) which did not belong to Govt. Though proved later on.