These sort of questions are easy to test by yourself. You should get familiar with console commands like 'r_speeds 0/1' and 'gl_wireframe 0/1/2', if you aren't already. They allow you to see how many world and model polygons are being rendered, and what parts of the level are currently drawn.
Most systems nowadays can handle world polycount of 1000, 1500, if not higher. Model polygons are generally 10 times cheaper to render, so if you can, modelling a new medkit is the better option. It saves you a lot of entity trickery after all.
Anyway, if you stick with a brush-based medkit, use a func_illusionary - the player can walk through it then - and killtarget it when the player walks through the pickup trigger. That will also permanently remove the entity from the game's memory. Not that a single entity gives much overhead, but oh well.