1) Your question may be answered if we look at the Mishnah Berurah in Bi'ur Halachah OC 208:19, DH Sulam. The Bi'ur Halachah cites the Bi'ur ha'Gra who sides with the Rashba, that the only prohibition is to transport the ladder from one place to another, while merely moving the ladder around in its place is permitted.

2) This means that according to the Rashba, the ladder is not actually Muktzeh. Rather, the prohibition involved is that if one moves it around between different chicken coops, this arouses a suspicion that one is going to do construction work on the roof. In contrast, merely carrying it a short distance is permitted.

3) This is why one may use the hammer to crack open nuts. The only activity which is prohibited, according to the Rashba, is conspicuous transporting of this noticeable ladder, while merely moving around a hammer does not arouse suspicion that one is going to build with it; the only forbidden activity is moving around a large object from one place ready for construction to another similar place.

Kol Tuv,

Dovid Bloom

Here are more differences between the ladder and the hammer:

1) a. Tosfos (Beitzah 9b, DH Mai) makes a distinction between different kinds of ladders. Tosfos presents a contradiction to the Gemara in Beitzah from the Gemara in Eruvin (77b) which states that it is permitted to move ladders. He answers that the Sugya in Beitzah is referring to large ladders, and that is why it is forbidden to carry them, while the Sugya in Beitzah refers to small ladders which one may move around.

b. According to this, since a hammer is a small item, it is permitted to move it around. The only item for which we are concerned that people will say he is going to use for construction work is a large ladder, while people will not find his activity with the small hammer so noticeable and will not suspect him.

2) a. Another distinction can be seen in the Mishneh Berurah OC 308:80 in the name of the Pri Megadim who writes that, according to the Rambam, one may not move the ladder used for climbing on the roof, even "l'Tzorech Gufo u'Mekomo" -- even if one is moving the ladder in order to use it, or if one needs to use the place where the ladder is situated for some purpose.

b. What this means is that according to the Rambam, the ladder is not even considered a "Kli she'Melachto l'Isur" -- a utensil which is generally used for a forbidden Melachah. The Halachah for a Kli sh'Melachto l'Isur is that one may move it l'Tzorech Gufo u'Mekomo; this indeed is the reason why one may use the hammer to crack the nuts, because this is considered "l'Tzorech Gufo" as the hammer is a Kli and one is now using it for a permitted purpose.

c. The Magen Avraham OC 308:38 writes that the reason why the ladder is not considered a Kli according to the Rambam is that it is similar to the door of a house. A house is not a Kli, so its door is not a Kli, and similarly the ladder is not a Kli.

d. According to the above, we may now explain that when a person uses a hammer to crack nuts, he is in fact using a "Kli" for a permitted purpose. Therefore, we are not worried that people will think he is using the hammer for construction; people understand that a hammer does have permitted uses as well. In contrast, when somebody moves around a ladder, it is not considered a Kli and therefore we are more stringent with its Halachos and take into account forbidden activities that onlookers may think he is carrying out.

Kol Tuv,

Dovid Bloom

I posed your question to a Gadol and he replied "Patish Ikaro la'Kol" -- a hammer is intended for all purposes. I will attempt to explain this answer.

1) First, it is worth bearing in mind that nowadays we possess a wealth of different tools, each one having a specialized use. In the time of the Gemara there was probably less of a choice of different tools for each particular job. It is quite likely that there was no such thing as a nutcracker, designed explicitly for cracking nuts. Therefore, even though the majority of tasks done with a hammer would be activities which are forbidden on Shabbos, nevertheless it would not be unusual or remarkable to use a hammer to crack nuts if necessary. Therefore, Chazal did not make a prohibition because of Mar'is ha'Ayin to do so.

2) Even if we would say that nowadays it is unusual to crack nuts with a hammer, nevertheless we have a rule that in our times we do not make new decreees and prohibitions that were not made by Chazal. In addition, it appears to me that even nowadays it would not be so unusual to use a hammer for such a purpose. For instance, if somebody did not have a nutcraker available, it is very likely he would use a hammer instead, so even nowadays there would be no need to make a prohibition on such a thing.

3) In contrast, it appears that the ladder referred to in the Gemara here had a much more specialistic use. This can be seen more clearly if we look at the Chidushei ha'Rashba to Beitzah 9b, DH v'Yesh, who cites an opinion that the Gemara here is discussing very large ladders which are usually used only to go up on the roof to smear on material there. According to this, there certainly is a very big difference between these ladders and the far more versatile hammer.

Kol Tuv,

Dovid Bloom