No skill points are gained during the negative effect. They are gained all at once the moment the effect expires.
Amount of skill point gain largely depends on how long the negative effect lasts.
Max Energy has a minor 5-minute stress resistance debuff, so drinking one every 5 minutes is a cost-effective way to gain skill points.
Meldonin injector has multiple minor 15-minute debuffs, be sure to bring extra food & drinks as it drains your energy and hydration.
"Obdolbos 2" cocktail injector has multiple 30-minute debuffs. It can be employed on longer raids or if your Immunity and Metabolism are high level. Be sure to bring extra medkits, as it causes you you to lose health.