90minutes seems quite reasonable for check-in for somebody with checked luggage at most airports - I certainly wouldn't say this was extreme. Some airports are 60minutes but 90minutes I think is the norm.
In terms of your connection, if the flight is with EK or on the same ticket then yes they will 'look after you' so to speak if you miss departure. However, the fact you've mentioned the checkin desk suggests you need to collect your bags and re-check them in which might mean the flights are on separate tickets. Therefore Emirates won't accommodate you, see you as a no show, and cancel your ticket. If you wish to travel you will probably be expected to pay for another ticket. If you are worried about this I would suggest getting good travel insurance which covers situations such as this.