Court marriage- 2 witness can't come on marriage date for some medical emergency

Inform to the marriage registrar about the abscentees of witnesses. Follow according to his instructions.

Yes.  Any 3 majors who are known to you may sign as witnesses.

Whether the subject Court marriage under the provisions of Section 5 & 6 of Special Marriage Act, 1954 as notice for intending marriage ??

or

Registration of marriage under the provisions of Section 8 of the Hindu Marriage Act, 1955 ???

Under Special act marriage 1954. 

Originally posted by : Parshant Garg

Under Special act marriage 1954. 
Yes you are right.
Online Court Marriage

As the name suggests, Special Marriage Act is a ‘Special’ legislation in India, which enable a special form of marriage for couples following different religions, or desiring a civil form of marriage.

The Act allows solemnization and registration of marriages which couldn’t be solemnized under the various religious customs. For example,  two Indian citizens having different religions can get married under this Act.

An  Indian  citizen and his/ her foreign national partner can also get married under the Act. Even two  foreign  nationals can get their marriage solemnized and registered under the said Act as observed by the Delhi High Court in a recent judgment in the case of Bhumika Mohan Jaisinghani and Anr. v/s Registrar of Marriage and Ors.

Accordingly provisions of Special Marriage Act, 1954 cannot be invoked for solemnization and registration of marriage by a Hindu couple.