Actually there are two aspects to the ion-exchange issue. The first is the kinetics for a charged analyte to bind and then dissociate from a charge on the surface. This is pretty much the same in HILIC and regular ion-exchange. The second is the rate at which a charged analyte can exchange counterions during the chromatography (which seems to be what Petrus is addressing and what Adam is apprehensive about). Adam is correct to be concerned. Take a look at Fig. 14 in Anal. Chem. 80 (2008) 62, per the following link:
http://pubs.acs.org/doi/pdf/10.1021/ac070997p
This is an extreme case of the kind that Adam described; a charged analyte that elutes in HILIC in two well-separated peaks with a continuum between them. One peak corresponds to the analyte with a counterion different from the one in the mobile phase while the other corresponds to the analyte molecules that exchanged their counterions for the one in the mobile phase at the start of the migration through the column. The two ion pairs differ in polarity (which is something that HILIC is sensitive to) and hence migrate through the column at different rates. The continuum consists of molecules of the analyte that started with one counterion and exchanged it for the other counterion sometime during the migration. A less severe case would feature a badly skewed peak rather than two separate peaks (Adam's "smear").
The example in the figure was obtained with 10 mM salt in the mobile phase, a common concentration in HILIC. Obviously counterion exchange is quite slow under those circumstances. If the concentration in the mobile phase had been, say, 100 mM, then the exchange of counterions would have been 10x faster and the problem less severe. A more convenient solution would be to make sure that charged analytes are paired with the same counterions as the one(s) in the mobile phase before injection. If that's inconvenient to implement, then I'd recommend adding to the sample a solution that contains a lot of the salt that's in the mobile phase. That way, the counterion exchange can be completed prior to injection.
Incidentally, that 2008 paper provides a number of reasons why some HILIC analyses won't go well unless there's some salt in the mobile phases.
Regarding Adam's other issue: No, don't try dissolving a salt in 100% ACN. Either it won't dissolve or you might get phase separation, per Per-Åke Albertsson's work. You would be much better off if the reservoir for Mobile Phase A contained the solution that you actually plan to use for Mobile Phase A, i.e., with some water. That should alleviate your solubility problem. It will also preclude any problems from trying to mix, online, the low-viscosity ACN with the higher viscosity Mobile Phase B, and will permit any degassing to occur offline. Please answer the following questions:
1) Why do you have to start with 100% ACN in the reservoir? Let's hear your long story.
2) Salt selection: Which is more important: volatility or transparency at low wavelengths?