For words in the variables $X$ and $Y$ satisfying the commutation relation of the $q$-deformed generalized Ore algebra, $XY-qYX= μI + νY$, we show that the corresponding normal ordering coefficients can be given an interpretation in terms of mixed placements of rooks and files. In particular, the associated $q$-deformed Ore-Stirling and Ore-Lah numbers are treated in detail. We show that the $q$-deformed Ore-Stirling numbers (resp., $q$-deformed Ore-Lah numbers) are given as mixed placement numbers of rooks and files on the staircase board (resp., Laguerre board). Using this combinatorial interpretation, their recurrence relations are derived. In addition, the normal ordered form of the binomial $(X+Y)^m$ in the $q$-deformed generalized Ore algebra is determined. These considerations are then extended to the $q$-deformed polynomial Weyl algebra generated by $X$ and $Y$ satisfying $XY-qYX=f(Y)$ for some polynomial $f\in \mathbb{C}[Y]$. In particular, associated $q$-deformed polynomial Stirling and Lah numbers are introduced and their properties studied. The normal ordered form of the binomial is also extended to the $q$-deformed polynomial Weyl algebra.