can defence struck of application lies if written statement not filed within 90 days in 125 crpc

No, Court can grant more time to file written statement if non petitioner satisfy the court sufficient reason.

Unlike the provisions of Civil Procedure Code, Criminal Procedure Code has no laid down any time frame. As such the reply ought to be filed within the time frame set or granted by the Court. Willful disregard and/or chronic negligence could lead the defense being struck off,