Does killing scientists affect anything?

Yes it do :) For example there is a guy in alpha labs in reactor chamber he ask You to open it - if You activate it he will die, if You open it he will left this room and unlock small room with a lot of ammo and guns in next corridor. Another example - map second level, map mars underground - when they open portal to hell and You are on Your way to mars city there is scene when zombie kill scientist and he fall (it is in room with 3 monitors, one show message "Valve error"). If You kill zombie, scientist will run away and soon You will find unlocked cabinet with additional armor. Sometimes scientist only have codes to lockers or nothing. If You kill them game will ends in normal way.