Of course the German plan took into account military as well as political considerations. Whether the latter were accurate or not, it doesn't matter. The fact is that, if the political plan was to drive a wedge between the Czechs and the Slovakians, cutting the country in two, invading the Czechs, and not attacking the Slovakians made a lot of sense.
Assuming this political side of things came to fruition for the Germans, then obviously there would be no need for an attack along the short path from Vienna to Bratislava.
Assuming on the contrary that the political effects did not turn to Germany's liking, then at least a demonstrative operation there, possibly with reserve units, would have made sense.
There was no need for it because if German pincer movement into Moravia from North and South worked, Germans would basically bagged most of Czechoslovak Army in Moravia and Czech lands. There would be only 3rd Czechoslovak Army left plus some divisions from Moravia which would managed to retreat to Slovakia. Fight would go on little bit longer at Czech lands and then it would be over. Morava river border between Austria and Slovakia was not well suited for attack. It's wet full of marshes etc. Even when you look on todays map there are marshes marked. At the time Morava was much less regulated. Of course when river is regulated some dams and regulation works could be destroyed and area flooded again.
So people have to make their minds up.
Do they want the Slovakians to support Czechoslovakia, Slovakian soldiers to show up at their barracks when mobilized, etc.? Then a significant chance exists that operations take place against Bratislava, a city inconveniently near an international border with the enemy. This is, BTW, the outcome I find more likely.
Or do they want no attack towards Bratislava or against Slovakia in general? Then that is probably a sign that Czecho... Slovakia is coming undone at the seam.
If you mean people on this forum, well people do not really need to make their minds. It was done for them OTL 1938.
Slovak and Ruthenians soldiers during September 23rd mobilization showed up in their barracks! There were no incidents or refusals to fulfill orders of commanding officers. Well to be honest, if I remember correctly there was one incident when some soldier after being punished for something he did on his free time in local village killed his officer. That was however criminal offense and had not some political background. Shet like this happens sometimes when you give people guns.
According to memories of Czech officers serving in Slovakia even Hungarians showed up mostly without problem. So mobilization in Slovakia went without problem and as a matter of fact after Andrej Hlinka death leaders of Slovak Hlinka's People Party called Slovaks to support Prague in just defense of Czechoslovakia. That's according to leading Slovak military historian Dr. Caplovic. Yes Slovaks wanted autonomy as was promised to them at Czech-Slovak negotiation in USA in 1918. Nothing wrong with that.
Interestingly even after Munich, and after Slovak autonomy was finally granted, future Slovak PM and future Slovak president Tiso asked and basically begged Prague not to cede Slovak territory to Hungarians or Poles but to fight.
Of course if Czechoslovak army was defeated there would be probably some push from Slovak side to try pick up the pieces and settle with Germany and Hungary. Would Germans be interested after wards is hard to say. For Germans politically would be still good to settle with some rump Slovak state as it would somehow show rest of Europe Czechoslovakia fell not just from outside but also from inside. If Hungarians do not attack it would also keep Romanians and Yugoslavians out of equation. And Romanians did put more troops on Hungarian border in September 1938 basically tying Hungarians, and even in March 1939 OTL. But that wouldn't make difference any more if Czechoslovak army was defeated. Also without France and Britain all Czechoslovak military aims are out. Czechoslovakia can't defend everything and there is no much sense to retreat to Slovakia and continue fighting. Of course if Czechoslovakia managed to blunt or defeat German northern and southern thrust and keep German advance west slow, France may either jump in after successful initial defense or Hitler is removed and that would change situation.
Other option would be of course, if Germans get really bad bloody nose and Germans, after pushing Czechoslovaks out of Sudetland would offer negotiations again on pretense their military and political aims were achieved and that's is all they wanted.
That is another interesting scenario. How would situation develop afterwards in 1939? Same as OTL? Sudetenland is lost however unity of Czechs and Slovaks is confirmed in the fight. Even morale of the people would be higher - something like "We were beaten but look at other guy". OTL Czechoslovak army, after Benes agreed with Munich, was leaving fortifications and positions with low morale, there were suicides among soldiers and officers etc. Actually there were worries among politicians that some unit(s) may not fulfill the orders and start the fight on its own. It happened in March 15th 1939 but more due to miscommunication. Garrison was not informed Germans were allowed in.