From the Bernoulli equation for a constant-density fluid,
$$
P + \frac12 \rho v^2 + \rho g h =\text{constant}
$$
you can see that the “vertical pressure” $\rho g h$ at some point is the same as the weight of a vertical column of the fluid divided by the area of that column. A cubic meter of air at sea level has a mass of about a kilogram. If the atmosphere had constant density with altitude, you could get $10^5\rm\,Pa$ at sea level from a pile of stationary air with height $10^4\rm\,m$. A better model of the atmosphere has the density falling off exponentially as you rise; however the “scale height” of this exponential is in fact approximately ten kilometers.
That is to say, the sea-level pressure of $10^5\rm\,N/m^2$ occurs because a meter-squared column of air, from Earth’s surface to space, has a mass of about $10^4\rm\,kg$.
In your question about a mass on a scale, you don’t ordinarily observe an effective-mass difference between horizontal and vertical objects. If you were somehow able to remove the air between your horizontal plate and the scale, most scale designs wouldn’t change the effective mass either. However, if you remove the air between the scale and the plate, then try to pull the plate and the scale apart, you would find that it takes ten tons of effort to pry them apart.
Normal people refer to this effect as “suction,” but it is actually the weight of the atmosphere trying to push its way into gaps. Note that suction forces can point in directions other than “down.”
The primary way that the atmosphere affects objects’ weight is via buoyancy. Consider a helium balloon, which has positive mass: if you tie it to a scale it will float up instead of pushing down, so its effective weight is negative. For objects with densities much greater than air (such as water, $\rho_\text{water} = 10^3\,\rho_\text{air}$), the buoyancy effect is frequently negligible.