T 3 Questions

A married couple held all of their investment jointly and at the end of 2018 the wife died.
Q1) since the assets were held jointly with rights of survivorship, the transfer of these assets to the husband would not go through the estate of the wife, but would become the property of the husband. Is this correct?

Are you asking an Estate Asset question, or a Tax question?
The answer to your question may not be that relevant from the point of view of the 2018 tax return of the wife. Also, the beneficial ownership prior to death could have been be almost any percentage.
.
.
Q2) If the above is wrong and there was a deemed disposition on date of death and the Fair Market Value at the time of death was a capital loss, does this need to be reported on her return? She is not able to claim this loss even in the year of death.

Again, the answer to Q1 is likely not relevant from the point of view of the 2018 tax return of the wife. If she had any beneficial ownership in 2018, then she had a disposition in 2018.
.
.
Q3) I have prepared a T3 return, as there was a T5 and two T5008 slips issued for 2019. Is there a way of filing this return without having a trust account number?

You cannot file a T3 return without that T3 return being assigned a Trust tax number.
.
You probably want to review ITA S70, particularly S70(5) and 70(6).
The general rule would be FMV, but for spouses could be ACB.

Estate matters can be extremely tricky, challenging, and complex on occasion…

If the T1-2018 (final) for the wife has not yet been filed, then it is seriously late at this point…

Presumably the Executor of the Estate pursuant to the Will is the surviving husband? What does the will say? Has the Executor made any distributions pursuant to the will? What were they? How much? what date? Is the foregoing properly documented in the Estate accounts and records?
The Estate may have income, or it may not. Income on assets accruing/paid to beneficiaries may have to be reported in 2019 tax year.

The mere existence of T5s and T5008 does not necessarily mean the the Financial Institution has them exactly correctly allocated to the correct taxpayer, since they have a complete absence of information as to the administration of the Estate.