HI Pruth and Welcome to MySwissAlps
Q1. Am I correct that there is no Glacier Express during this time?
Q2a. What is the alternative train to Zermatt with the best scenic route?
A2a. There are regular trains which follow the Glacier Express Route. Use the timetable (www.myswissalps.com/ti metable) to check for trains from St Moritz to Zermatt via Filisur, Chur, Disentis/Müster (or Andermatt).
Q2b. Is St. Moritz to tirano to lugano to zermatt possible ?
A2b. Yes but it is a long way round and the Bernina Express Bus Tirano to Lugano does not run at that time of year so would need to take train Tirano to Milan then to Zermatt via Domodosola. Italian train Tirano to Domoodosola is not covered by your Swiss Travel Pass. Or you can go Milan (or Monza) to Göschenen then to Andermatt and pick up Glacier Express route there.
Q3. Is there a reason the train does not operate during this time?
A3. Break between Summer and Winter seasons?
Q4a. We also plan on using Golden pass express, and Wilhem tell express in remaining part of our journey, does these trains operate definitively during the dates we will be in the country?
A4a. Golden Pass Line trains do but William Tell (now renamed Gotthard Panorama Express) does not. It is summer only. You can take regular train on Lugano to Luzern route though if you go via Göschenen.
Q4b. Also, do I need reservations on each of these trains?
A4b. Not compulsory and probably not required at that time of year.
Q4c. And, how do visit www.sbb.ch how do I know which of the train is one of these scenic trains, are there any identification codes that go with these trains?
A4c. The Bernina Express is designated BEX, the Golden Pass (Zweisimmen to Montreux) is MOB on the timetable.
Q5. Last question is, what is a standard view train v/s barrier-free view train?
A4. If you mean panoramic versus regular trains then the difference is not as great as you would imagine. The Panoramic BEX is nice and so is Golden Pass.
Hope that helps.
By the way have you checked the timetable for your planned "Neuchatel -> Engelberg -> Mt. Titlis -> St. Moritz". That's a big day trip!