If a bacteria has a diffusion barrier in its capsule, which prevents harmful substances from entering in it, then how do antibiotics affect bacteria?

Many antibiotics work by diffusing across the cell wall, affecting the machinery involved in the formation of the cell wall, causing damage to DNA first and then impeding it. Further information on this can be found here.

The article quotes "some antibiotics, particularlyβ-lactams, pass across the outer membrane through the water-filled channels of a class of proteins called porins." This indicates that the diffusion method is not the only way that antibodies enter bacterial cells.

There are other ways by which bacteria can even combat the antibiotics entering through porins, such as reducing the density of the porins in the cell wall, making these porins less susceptible to the antibiotic using the porin. These porins become the alternative ways for antibiotics to enter the bacterial cells. Once they enter the cell, they cause damage in any of the three ways mentioned above.

Antibiotics can still impact bacteria with diffusion barriers by targeting specific cellular components, such as cell walls or protein synthesis, disrupting essential processes and causing bacterial death.