A lot will depend on who might be buying the company, and whether the primary aim is to sell the company or not, how tightly your code is dependent on the GPL code, and whether you have customised the GPL code.
I have run into a number of companies that have absolute "no GPL software" policies - typically these are companies from an embedded background, and it will (at best) take some effort to explain why the GPL is not such a problem on server side software.
You can probably also expect a higher level of technical due diligence than if you were not using GPL software - when an acquirer is being expected to pay out a large sum of money, they will want to be sure whether or not your software is a "derivative work" of the GPL code or not.
Another potential issue would be that you may well be unable to give a potential acquirer a copy of your code to look at prior to the acquisition - as in the general case this would count as "distribution", and you would then either have to give them the whole code under the GPL or be at risk of the copyright holders of the GPL code suing you for infringement.
Your company will have to assess the risk for itself, and if it is actively trying to sell itself then this should be done as soon as possible.