The rule says you add your proficiency bonus to spell attack rolls, so you do.
It's not missing from the table, it's just in another table on page 95, along with all the other core Rogue numbers. Spellcasters usually have spells as a core feature and they have all their level-based numbers in one table (see the Sorcerer just a few pages further on, on page 100). The Arcane Trickster though is a set of added abilities on top of Rogue. Rogues don't normally get spells, so the stuff that's normally in one table for a spellcaster — including proficiency bonus and spells known/slots — is for an Arcane Trickster split across the Rogue table and the Arcane Trickster table.
Looking at it another way: it wouldn't make sense to repeat Proficiency Bonus in both tables (it would be a waste of expensive page space), and it wouldn't make sense to combine the tables (all the spell stuff would be confusing for non–Arcane Trickster Rogue players), so it makes the most sense to have these things separate. Proficiency Bonus is the same for every Rogue of a given level,1 so it goes in the main Rogue table; spell details are not the same for every Rogue, so they go in a separate table. Being in separate tables doesn't imply that Proficiency doesn't apply to the spells.
- Actually, Proficiency Bonus is the same for everyone of a given level regardless of class, but having a separate "everyone's Proficiency Bonus table" would just scatter the information around the book and make it that much harder to use. In this case, it's worth spending expensive page space repeating it, so that everything a class needs is in one place.