The differences are in size, shape and some performance characteristics. AT-cut crystal blanks are circular, and AT-strip cut crystal blanks are rectangular. Both types are AT-cuts, but several differences in performance characteristics exist because of the different geometry of the blanks.
In general, given the same frequency and overtone, the AT strip will have a lower value of Shunt Capacitance (Co) and Motional Capacitance (C1). It will also have a higher value of Effective Series Resistance (ESR) and Motional Inductance (L1). Because pullability is a function of Co and C1, AT strip cut crystals have less pullability than ocular AT cut crystals.
The HC49U crystal utilizes a circular AT cut crystal blank. Due to their small size, most surface mount crystals use a rectangular AT strip cut crystal blank. ("Strip" refers to the rectangular shape of the blank.)
While both are AT cut blanks, several differences exist due to their different geometry. In general, given the same frequency and overtone, an AT strip cut will have a lower Shunt Capacitance (CO) and Motional Capacitance (C1) than the AT cut. Because pullability is a function of the capacitance ratio CO/C1, AT strip crystals have less pullability.
Pullability is the amount by which the frequency of a crystal will change when the circuit condition is switched from series to parallel resonance.
Pullability is also used to describe the frequency change that occurs when the load capacitance is switched from one value to another.
I would not make the change without a thorough investigation. Some of the SMD (surface mount device) crystal units are comparable to conventional crystal units, others are not.
In general, SMD's have higher resistance, differing values of shunt and motional capacitance, and are more sensitive to drive level. The pullability characteristics of these devices may differ significantly from a conventional crystal.
I would recommend a fairly exhaustive qualification sequence before making the switch.
Drive Level - HC49U crystals are typically rated 1.0mW max, while the HC49S and most SMD crystals are rated at only 0.5mW or 0.1mW maximum. See question 11 for more information on exceeding the maximum drive level of a crystal.
Pullability -some applications require tuning the frequency of the oscillator, either by mechanically or electrically changing the value of load capacitance.
The HC49S and surface mount crystals have less pullability than the HC49U. It is important to verify whether the HC49S or the surface mount crystal will have sufficient pull range for the application. Generally, an HC49S has one half the pullability as an HC49U.
ESR - The Equivalent Series Resistance (ESR) is generally higher with the HC49S and surface mount crystals, and can cause a problem if the oscillator circuit does not have sufficient loop gain.