When are two signals orthogonal?
As you may know, orthogonality depends on the inner product of your vector space. In your question you state that:


  While sine and cosine are orthogonal functions...


This means that you have probably heard of the "standard" inner product for function spaces:

$$\langle f,g\rangle=\int\limits_{x_1}^{x_2} f(x)g(x) \ \mathrm{d}x$$

If you solve this integral for $f(x)=\cos (x)$ and $g(x)=\sin(x)$ for a single period, the result will be $0$: they are orthogonal.

Sampling these signals, however, is not related to orthogonality or anything. The "vectors" you obtain when you sample a signal are just values put together that make sense to you: they are not strictly vectors, they are just arrays (in programming slang). The fact that we call them vectors in MATLAB or any other programming language can be confusing.

It's a bit tricky, actually, since one could define a vector space of dimension $N$ if you have $N$ samples for each signal, where those arrays would indeed be actual vectors. But those would define different things.

For simplicity, let's suppose we are in vector space $\mathbb{R}^3$ and you have $3$ samples for each signal, and all of them are real-valued. In the first case, a vector (i.e. three numbers put together) would refer to a position in space. In the second one, they refer to three values a signal reaches at three different times. In this example it is easy to spot the difference. If you had $n$ samples, then the notion of "space" would be less intuitive, but the idea still holds.

In a nutshell, two signals are orthogonal if the inner product between them (namely, the integral I wrote above) is $0$, and the vectors/arrays obtained by sampling them tell us nothing about their being orthogonal.