Nether portal particles going through blocks

That's not a bug. The only "fix" would be to change the distance at which all particles for Nether Portals are displayed at.

Same issue but during day time

I think it shouldn't even escape it on 1-block-distance.

This is as intended. The point being that ender particles (which is what the portal is producing) are "teleport" particle and do not care wheter there is a solid block near them as they can pass through objects. Basically like when you throw an ender pearl over a hill... you pass through the hill when you teleport.

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Smoke from torches also can pass through solid blocks, in 1.6.4.