Except that 100% of any positive number is itself, so subtracting a number from itself would bring you to zero. Then 50% of zero is still zero, so you should stay at zero rather than go negative, yes!?
That depends entirely on how they set up multiplier stacking, and from everything I've seen in the game it appears that most percentage bonuses and maluses are additive, rather than multiplicative. This makes the actual modifier to your research (or experience, or whatever) equal to
(100 + bonus1 + ... + bonusN - malus1 - ... - malusM)%
of the base value (bonus1 to bonusN and malus1 to malusM are expressed as positive percentages, i.e. a 10% bonus is 10 and a 25% malus is 25), rather than
(base value)*(1 + total bonus expressed as a positive decimals)*(1 - total malus expressed as a positive decimals)
which would give you a system where you could not really cancel a 100% malus.