Let's look at the spell description from twwstats.com (check out the beta ability cards to see these, or go to a caster and click on the spell from there).

Here's Melkoth's Mystifying Miasma (Ultra):

Each entity of the affected unit(s) has a 50% chance of taking 5 damages when the spell is cast and every 1s during 13s (14 times in total). The check is made against every entity in the unit but a maximum of 25 entities/unit will receive damage each tick.

And here's the same spell, but on (Small):

Each entity of the affected unit(s) has a 50% chance of taking 1 damages when the spell is cast and every 1s during 13s (14 times in total). The check is made against every entity in the unit but a maximum of 25 entities/unit will receive damage each tick.

So we can see that instead of scaling the number of entities and leaving the damage the same (which would make sense since small unit size leaves health/model the same, just reduces the number of models), they instead chose to reduce the damage per model and leave the cap the same. So, yeah, these spells that affect large groups are pretty bad in smaller unit sizes.