It’s a long day for a day trip. 1h15 min is optimistic, even if you drive at night. During the day, in the morning, you might encounter some traffic on the surface streets in Como for sure. I’ve done that trip from Malpensa a few times (to go to Menaggio)..
I would plan 2 hours to get on time for whichever ferry you want, as you might need time to find parking.
I’ve downloaded the timetable for you (see PDF below), but for now only the winter timetable is available. You can check for the summer season at a later date.
The fast hydrofoil is the one with the red arrows on the timetable. The travel time to Bellagio is about 50 minutes. Not all runs stop at Varenna. Note that some run only on Sundays/Holidays (FESTIVO) some run on weekdays only (FERIALE) others run everyday both Sundays and weekdays (GIORNALIERO). Feriale in Italian means weekday and includes Saturday unless otherwise noted.
Another option is to forget about the hydrofoil from Como, and drive to Menaggio instead (an extra half hour). From Menaggio there are many ferries to both Bellagio and Varenna, and the ferry ride is only minutes. I’ve never taken the hydrofoil from Como but I’m not sure the hydrofoil permits to stay in top to take a nice view, you might be stuck in the hull. The regular ferry does permit to stay above, but it will take twice as long.
Be aware that the freeway A36 (Pedemontana Lombarda) is a toll freeway but there are no toll booths. The take a picture of your license plate then you have to go online and pay. So note the entrance where you enter and the exit. You have only a number of days to pay before they send a huge penalty to the rental car company (which you will have to pay). The link to pay is below. You can become familiar with the process even before you go and you can register ahead of time. Obviously you will need to add the license plate only after you have the car.
https://www.pedemontana.com/en/payment
Ferry timetable below:
https://www.navigazionelaghi.it/wp-content/uploads/2025/10/Orari_Web-I25-26.pdf