According to the nLab, Lawvere metric spaces occur rather naturally (that is as certain enriched categories). A Lawvere metric space is a set $X$ equipped with a function $d : X\times X \to [0,\infty]$, such that:
- $d(x,x) = 0$
- $d(x,y) + d(y,z) \geq d(x,z)$
I don't have any background in enriched category theory, so can only see the theory of Lawvere metric spaces on an elementary level.
Omitting the separation axiom, that is:
$$d(x,y) = 0 \Rightarrow x = y$$
seems to cause some weird things. Consider the category of Lawvere metric spaces, where a morphism $f : X \to Y$ is a function such that:
$$d(x,y) \geq d(fx,fy)$$
It is well known, that if it also an isometry, then $f$ is injective. But it appears that for Lawvere metric spaces you cannot prove that every isometry is even mono in the category of Lawvere spaces. I can only show that these maps are "almost" injective in the sense that:
$$fx \cong fy \Rightarrow x \cong y$$
where $x\cong y \Leftrightarrow d(x,y) = d(y,x) = 0$.
How can I view this "situation" (of isometries being "almost" mono / injective), such that it seems natural instead of "weird" and unwanted?
I assume you are looking for some real world examples of pseudo-metric spaces (that correspond to what you call Lawvere-metric spaces).
Well a family of examples is given by the $\mathcal L^p$-spaces (where $p$ is real number in $[1,\infty]$).
In general for $(\Omega,\mathcal F, \mu)$ a measured space, we have the vector space $\mathcal L^p(\Omega)$ whose elements are measurable functions $f \colon \Omega \to \mathbb R$ such that $$\int |f(x)|^p d\mu(x) < \infty\ .$$ To be exact $\mathcal L^p(\Omega)$ is a sub-space of the vector space $\mathbb R^\Omega$ of the real valued function defined over $\Omega$. What's more is that the mapping $$d \colon \mathcal L^p(\Omega)\times\mathcal L^p(\Omega) \to \mathbb [0,\infty)$$ defined by $$d(f,g) = \left(\int |f(x)-g(x)|^pd\mu(x)\right)^{\frac{1}{p}}$$ gives this space the structure of pseudo-metric space.
It is not a metric space because there are many functions in $\mathcal L^p(\Omega)$ that make null the integral $$\int |f(x)|^pd\mu(x)$$ while being not null.
Of course one can quotient these spaces to obtain some metric spaces, nonetheless it is important to consider these spaces at some point if one what to establish precise results for the $L^p(\Omega)$ spaces: the spaces obtained by the $\mathcal L^p(\Omega)$ identifying functions whose distance is zero.
Take a look to the link above for more informations.
Edit: I see that my answer didn't address your real question, allow me to make amend.
Let $p$ be as above and let $p' \in [1,\infty]$ be the only number such that $\frac{1}{p}+\frac{1}{p'}=1$.
By $\mathcal L^{p'}(\Omega)^*$ we will denote the space of continuous linear functionals defined over the space $\mathcal L^{p'}(\Omega)$.
Results on $\mathcal L^p$-spaces ensure that there is a linear map $$i \colon \mathcal L^p(\Omega) \to \mathcal L^{p'}(\Omega)^*$$ defined as $$i(f)=g \mapsto \int f(x)g(x)d\mu(x)\ .$$ This map is an isometry in your sense, still it is pretty important. Again if you pass this isometry to the quotient spaces ($L^p(\Omega)$ and $L^{p'}(\Omega)^*$ respectively) the you get a real-isometry between metric-spaces.
Another example of this strange isometry is the projection to the quotient $$\mathcal L^p(\Omega) \to L^p(\Omega)$$ as pointed out by Kevin Carlson below in the comments.
Hope this helps.