Many people have posted this "dings you for your deep stops" canard, but I've never been able to find a profile that does this.
When I do reasonable length deep stops, my dissolved gas model computer often clears the mandatory deco.
When I do excessively deep and long deep stops, both the pure dissolved gas models and the dual phase models appropriately add to the deco time. There are some slight differences, but nothing dramatic. Definitely not as dramatic as the effect of a rapid descent in some models.
Even though a neo-Haldanian computer shows that the ceiling depth is 10', you don't have to go zooming up there immediately.
You set the profile, the dive computer makes its best guess as to N2 loading.
As to the problem of computer failure during the ascent --- you have a gas plan that allows for a certain amount of maximum deco. You should remember what the total time to ascend was when you left the bottom. A reasonably alert diver should be able to complete his ascent and stops without difficulty, even if the computer dies during the ascent.