I think the inequality is true (assuming Choice, at least). I will make fairly heavy use of cardinal arithmetic/facts.
First, we can assume without loss of generality that $I$ is a limit ordinal, by passing to an appropriate cofinal subset (and because if $I$ has a maximum element, it's obvious). I will argue by proving a nice formula for the cardinality of each union.
Lemma. If $I$ is a limit ordinal and we have sets $A_i$ for each $i \in I$ such that $A_i \subsetneq A_j$ iff $i < j$, then $|\bigcup_i A_i| = \max\{|I|, \sup_i |A_i|\}$.
Proof. Let's write $A = \bigcup_i A_i$. There is an injection $I \to A$ given by sending $i$ to some element of $A_{i + 1} \setminus A_i$, so $|I| \le |A|$. It's also clear that for any $i$, we have $|A_i| \le |A|$. So $\sup_i |A_i| \le |A|$.
Conversely, we have $|A| \le |I| \cdot \sup_i |A_i|$, for example because if $S$ is a set of cardinality $\sup_i |A_i|$, then clearly $A$ injects into $I \times S$: for each $i$, choose an injection $\iota_i: A_i \to S$, and then for each $a \in A$, pick any $i$ such that $a \in A_i$ and send $a$ to $(i, \iota_i(a))$. But by cardinal arithmetic, $|I| \cdot \sup_i |A_i| = \max\{|I|, \sup_i |A_i|\}$, so this finishes the proof.
So now we know that $|\bigcup_i A_i| = \max\{|I|, \sup_i |A_i|\}$ and $|\bigcup_i B_i| = \max\{|I|, \sup_i |B_i|\}$. Since it's clear that $\sup_i |A_i| \le \sup_i |B_i|$, we are done.
I spent a bit of time looking for any reference to the above lemma on MSE, but I have not managed to find any. I am fairly sure it's true though..
Perhaps one reason it's hard to write down a proof is that there are counterexamples if you weaken things a bit - if you just ask for "$i \le j$ implies $B_i \subseteq B_j$", then there is a counterexample given by taking $A_i$ to be proper initial segments of $\omega_1$ and $B_i$ to all be $\omega$, for example. Also the example of "proper initial segments of $\Bbb Q$" gives some indication of why taking $I$ to be a limit ordinal was an important step - in that case the union $A$ is actually much smaller than $I$.
I have no idea what will happen in the absence of choice - that's above my pay grade. Here is some related discussion you may find interesting though.