Rules on attacking objects with magic say:
If an item is not carried or worn and is not magical, it does not get a saving throw. It simply is dealt the appropriate damage.
Rules on smashing objects further tell us that:
Acid and sonic attacks deal damage to most objects just as they do to creatures; roll damage and apply it normally after a successful hit. Electricity and fire attacks deal half damage to most objects; divide the damage dealt by 2 before applying the hardness. Cold attacks deal one-quarter damage to most objects; divide the damage dealt by 4 before applying the hardness.
With rare exception, the exact form the damage takes is not described by
the rules. People and objects just loose HP until they break / die. But we know that stone has hardness 8 and 15 HP per inch of thickness, so we can conclude that making 3-inch deep handhold requires making 45 HP worth of damage*, after dividers and hardness. If it is not stone, DM should approximate using materials in the table.
As for consequences, they are small. It takes a significant amount of spell slots and time to get similar effect rope ladder or rope with knots would gave. I bet your party will just bring one of those next time. It is a teaching moment on preparation, but it won't make your magic users just create stairs everywhere.
* As noted in comments, DM is empowered to use the rule that:
Very large objects have separate hit point totals for different sections.
45 HP is, by default, HP of 10 by 10 ft wall. You can divide it into a "handhold-sized" sections, substantially reducing damage needed. Also, unless your magic user is a skilled sculptor, you shouldn't allow handholds to be pretty. They will look like holes smashed in the rock, that's all. But indeed no reason they shouldn't give substantial circumstance bonus to the Climb check.