I use nexus mods (~mod folder) with steam workshop mods all the time with no issues or conflicts; but most of my mods are also purely graphical, so I can't say how the more intensive mods might behave with each other in regards to specific load order requirements.

im talking about the mods you subscribe on steam are they compatible with the mods you get on nexus . like the shay mods on steam doesnt have reduced weapon wear because im getting tired of repair cost and they jamming up after 2 mags of armor piercing ammo

It all boils down to what files each mod are using to get their job done. If two separate mods (regardless of where you got them) are trying to use the same files, that's when the most problems arise and you will find the most incompatibilities. All my nexus mods work fine with my steam mods because they all change different files.