Sorry for so long unreplying.
if you need your vias covered by mask (the green, or black,white,red,blue,purp,yellow layer that blocks the copper from soldering)
exported the maskTop.gts and maskBottom.gbs with vias deleted for sure,
sometimes the PCB manufacturer can choose the vias to be covered, mostly they follow your gerber
always check your exports with gerber viewer or with a pdf version,
they'll show if your mask/silkscreens were intended, or not.